Problem: pseudogenes/invalid genes stall downstream analysis with BV-BRC genomes
Summary
Genome 1282.2719 contains at least 25 CDS features whose translated sequence has an internal premature stop codon — i.e., verifiably non-functional/pseudogenized ORFs — none of which are reflected in any BV-BRC-reported metadata field. The GFF's own pseudogene feature-type annotation reports 0 for this genome, and the genome-summary partial_cds/partial_cds_ratio fields also report 0. This genome additionally lacks ##sequence-region header lines in its GFF3 (present in every other genome we checked) and uses self-referential placeholder contig IDs (see below), suggesting it was processed through an older or different annotation pipeline than typical current BV-BRC submissions.
Evidence
Method summary (the "how")
| Source | What it measures | How we computed it |
|---|
| GFF pseudogene feature type | Genes BV-BRC's own annotation pipeline explicitly labeled pseudogene in column 3 of the .PATRIC.gff | grep -c $'\tpseudogene\t' <genome>.PATRIC.gff |
BV-BRC partial_cds | BV-BRC's own summary-stats field for incomplete/partial CDS calls | p3-all-genomes --eq genome_id,<id> --attr partial_cds,partial_cds_ratio |
| Panaroo invalid-gene count | CDS whose translated sequence contains an internal premature stop codon (checked by actually translating each CDS, not reading any annotation field) | Ran panaroo --remove-invalid-genes --refind-mode off, grepped its stderr for "invalid gene! ... Has stop: True", and counted per source GFF |
Comparison table
| Genome | Contigs | GFF pseudogene count | BV-BRC partial_cds | BV-BRC partial_cds_ratio | BV-BRC hypothetical_cds | Panaroo invalid-gene count (ours) |
|---|
| 1282.2719 | 4 | 0 | 0 | 0 | 553 | 25 |
| 1282.3129 | 103 | 0 | 0 | 0 | 525 | 0 |
| 904315.3 | 144 | 18 | 0 | 0 | 566 | 0 |
| 904320.3 | 87 | 59 | 0 | 0 | 600 | 0 |
| 904330.3 | 56 | 47 | 0 | 0 | 439 | 0 |
| (remaining 12S. epidermidisgenomes) | 36–90 | 18–34 | — | — | — | 0 |
| (all 73S. argenteusgenomes) | 10–30 | — | — | — | — | 0 total (all 73 genomes) |
How we found it
We were debugging a severe Panaroo pangenome-construction slowdown (see context below) and, while testing panaroo --remove-invalid-genes in isolation, found that Panaroo's own CDS-translation check flags 25 genes in 1282.2719 as invalid due to internal stop codons. Cross-checking against BV-BRC's reported fields for the same genome (p3-all-genomes --eq genome_id,1282.2719 --attr partial_cds,partial_cds_ratio) returned 0 for both, and the GFF3 file itself contains zero features labeled pseudogene.
Reproduction
# Genome: 1282.2719 (Staphylococcus epidermidis strain CSF41498)
# GFF: fetched via BV-BRC CLI, p3-genome-fasta / genome GFF export
# BV-BRC-reported fields (all 0, despite the genes below being demonstrably broken):
p3-all-genomes --eq genome_id,1282.2719 --attr genome_id,cds,partial_cds,partial_cds_ratio,hypothetical_cds
# → 1282.2719 2490 0 0 553
# Genes independently confirmed to contain an internal premature stop codon
# (verified by translating the CDS sequence directly, via Panaroo v1.5.1's
# `--remove-invalid-genes` check):
fig|1282.2719.peg.62, peg.134, peg.219, peg.273, peg.438, peg.627, peg.656,
peg.657, peg.672, peg.993, peg.997, peg.1410, peg.1434, peg.1714, peg.1722,
peg.1796, peg.1808, peg.1917, peg.2000, peg.2115, peg.2305, peg.2378,
peg.2465, peg.2478, peg.2481
Additional annotation-pipeline inconsistencies on this genome
- Missing ##sequence-region header lines in the GFF3 (present on every other genome we checked in this species).
- Contig identifiers behave like real NCBI accessions (CP030246 etc.) rather than the synthetic placeholder pattern (<genome_id>.con.NNNN) seen on other older-pipeline genomes — so this isn't simply "unassembled," it's specifically the pseudogene/partial-CDS annotation that's missing.
Why this matters
Consumers relying on partial_cds/pseudogene fields to filter low-quality or degenerate gene calls (e.g., for pangenome analysis, comparative genomics, or QC pipelines) will silently retain genomes with substantial numbers of non-functional gene calls that these fields were designed to flag. In our case, this caused a severe (>100x) performance degradation in a downstream tool (Panaroo) that trusts gene-level input and only detects the problem via a full CDS translation check — something most consumers of BV-BRC data won't run themselves.
Ask
Could BV-BRC confirm whether partial_cds/pseudogene calling was skipped or failed for this genome's annotation run, and whether other genomes from the same submission batch/pipeline version are similarly affected?
Problem: pseudogenes/invalid genes stall downstream analysis with BV-BRC genomes
Summary
Genome 1282.2719 contains at least 25 CDS features whose translated sequence has an internal premature stop codon — i.e., verifiably non-functional/pseudogenized ORFs — none of which are reflected in any BV-BRC-reported metadata field. The GFF's own pseudogene feature-type annotation reports 0 for this genome, and the genome-summary partial_cds/partial_cds_ratio fields also report 0. This genome additionally lacks ##sequence-region header lines in its GFF3 (present in every other genome we checked) and uses self-referential placeholder contig IDs (see below), suggesting it was processed through an older or different annotation pipeline than typical current BV-BRC submissions.
Evidence
Method summary (the "how")
pseudogenein column 3 of the.PATRIC.gffgrep -c $'\tpseudogene\t' <genome>.PATRIC.gffpartial_cdsp3-all-genomes --eq genome_id,<id> --attr partial_cds,partial_cds_ratiopanaroo --remove-invalid-genes --refind-mode off, grepped its stderr for"invalid gene! ... Has stop: True", and counted per source GFFComparison table
partial_cdspartial_cds_ratiohypothetical_cdsHow we found it
We were debugging a severe Panaroo pangenome-construction slowdown (see context below) and, while testing panaroo --remove-invalid-genes in isolation, found that Panaroo's own CDS-translation check flags 25 genes in 1282.2719 as invalid due to internal stop codons. Cross-checking against BV-BRC's reported fields for the same genome (p3-all-genomes --eq genome_id,1282.2719 --attr partial_cds,partial_cds_ratio) returned 0 for both, and the GFF3 file itself contains zero features labeled pseudogene.
Reproduction
Additional annotation-pipeline inconsistencies on this genome
Why this matters
Consumers relying on partial_cds/pseudogene fields to filter low-quality or degenerate gene calls (e.g., for pangenome analysis, comparative genomics, or QC pipelines) will silently retain genomes with substantial numbers of non-functional gene calls that these fields were designed to flag. In our case, this caused a severe (>100x) performance degradation in a downstream tool (Panaroo) that trusts gene-level input and only detects the problem via a full CDS translation check — something most consumers of BV-BRC data won't run themselves.
Ask
Could BV-BRC confirm whether partial_cds/pseudogene calling was skipped or failed for this genome's annotation run, and whether other genomes from the same submission batch/pipeline version are similarly affected?