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BLASTn output format 6

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

blastn  -query genes.ffn  -subject genome.fna  -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., gene) sequence id
 2.  sseqid  subject (e.g., reference genome) sequence id
 3.  pident  percentage of identical matches
 4.  length  alignment length
 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 pident qlen length mismatch gapope evalue bitscore"

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"

  by Ian Korf, Mark Yandell, and Joseph Bedell