BLASTn output format 6

BLAST software tool

BLASTn maps DNA against DNA, for example gene sequences against a reference genome

blastn -query genes.fasta -subject genome.fasta -outfmt 6

BLASTn tabular output format 6

Column headers:

qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

1. qseqid query (e.g., unknown gene) sequence id

2. sseqid subject (e.g., reference genome) sequence id

3. pident percentage of identical matches

4. length alignment length (sequence overlap)

5. mismatch number of mismatches

6. gapopen number of gap openings

7. qstart start of alignment in query

8. qend end of alignment in query

9. sstart start of alignment in subject

10. send end of alignment in subject

11. evalue expect value

12. bitscore bit score

Define your own output format

by adding the option -outfmt, as for example:

-outfmt "6 qseqid sseqid evalue"

supported format specifiers are:

qseqid Query Seq-id

qgi Query GI

qacc Query accesion

qaccver Query accesion.version

qlen Query sequence length

sseqid Subject Seq-id

sallseqid All subject Seq-id(s), separated by a ';'

sgi Subject GI

sallgi All subject GIs

sacc Subject accession

saccver Subject accession.version

sallacc All subject accessions

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

qseq Aligned part of query sequence

sseq Aligned part of subject sequence

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

btop Blast traceback operations (BTOP)

staxids Subject Taxonomy ID(s), separated by a ';'

sscinames Subject Scientific Name(s), separated by a ';'

scomnames Subject Common Name(s), separated by a ';'

sblastnames Subject Blast Name(s), separated by a ';' (in alphabetical order)

sskingdoms Subject Super Kingdom(s), separated by a ';' (in alphabetical order)

stitle Subject Title

salltitles All Subject Title(s), separated by a '<>'

sstrand Subject Strand

qcovs Query Coverage Per Subject

qcovhsp Query Coverage Per HSP

default values are:

-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"

See also

blastn -help


BLAST-Glossary

BLAST-Command-Line-Applications-User-Manual

www.metagenomics.wiki