BLASTn output format 6

BLAST software tool

 BLASTn maps DNA against DNA, for example: mapping a 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 or source (gene) sequence id

   2.  sseqid      subject or target (reference genome) sequence id

   3.  pident      percentage of identical positions

   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