BLAST Output Formats

Currently three of the native BLAST output formats are supported:

Description	legacy BLAST	BLAST+	lambda extension
pairwise	-m 0	-outfmt 0	.m0
tabular	-m 8	-outfmt 6	.m8
tabular with comment lines	-m 9	-outfmt 7	.m9

Custom columns

For the tabular and tabular with comments lines formats you may specify the order and column composition. The columns have the same specifiers as in BLAST+, right now all of the above are supported via the command line option --output-columns. Please note that it is recommend to keep the first 12 columns as they are for compatibility, i.e. first write std and then custom columns that you want, e.g.--output-columns "std score qframe".

specifier	description	since
std	Default 12 columns (Query Seq-id, Subject Seq-id, Percentage of identical matches, Alignment length, Number of mismatches, Number of gap openings, Start of alignment in query, End of alignment in query, Start of alignment in subject, End of alignment in subject, Expect value, Bit score)
qseqid	Query Seq-id
qlen	Query sequence length
sseqid	Subject Seq-id
slen	Subject sequence length
qstart	Start of alignment in query
qend	End of alignment in query
sstart	Start of alignment in subject
send	End of alignment in subject
evalue	Expect value
bitscore	Bit score
score	Raw score
length	Alignment length
pident	Percentage of identical matches
nident	Number of identical matches
mismatch	Number of mismatches
positive	Number of positive-scoring matches
gapopen	Number of gap openings
gaps	Total number of gaps
ppos	Percentage of positive-scoring matches
frames	Query and subject frames separated by a '/'
qframe	Query frame
sframe	Subject frame
staxids	Subject taxonomy ID(s) seperated by ; (Taxonomic Workflows)	1.9.2
lcaid¹	Lowest common ancestor name (Taxonomic Workflows)	1.9.2
lcataxid¹	Lowest common ancestor taxonomy ID (Taxonomic Workflows)	1.9.2

¹ Not part of NCBI Blast.