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
-outfmt "6 qseqid sseqid pident qlen length mismatch gapope evalue bitscore"
supported format specifiers are:qseqid
Query Seq-idqgi
Query GIqacc
Query accesionqaccver
Query accesion.versionqlen
Query sequence lengthsseqid
Subject Seq-idsallseqid
All subject Seq-id(s), separated by a ';'sgi
Subject GIsallgi
All subject GIssacc
Subject accessionsaccver
Subject accession.versionsallacc
All subject accessionsslen
Subject sequence lengthqstart
Start of alignment in queryqend
End of alignment in querysstart
Start of alignment in subjectsend
End of alignment in subjectqseq
Aligned part of query sequencesseq
Aligned part of subject sequenceevalue
Expect valuebitscore
Bit scorescore
Raw scorelength
Alignment lengthpident
Percentage of identical matchesnident
Number of identical matchesmismatch
Number of mismatchespositive
Number of positive-scoring matchesgapopen
Number of gap openingsgaps
Total number of gapsppos
Percentage of positive-scoring matchesframes
Query and subject frames separated by a '/'qframe
Query framesframe
Subject framebtop
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 Titlesalltitles
All Subject Title(s), separated by a '<>'sstrand
Subject Strandqcovs
Query Coverage Per Subjectqcovhsp
Query Coverage Per HSP
default values are:-outfmt "
6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"