Headers

Headers are included in outputs for the samtools coverage command and blast results. Header definitions are as follows:

samtools coverage headers

Column header	Meaning
rname	Locus name
numreads	Number reads aligned to the region (after filtering)
covbases	Number of covered bases with depth >= 10
coverage	Percentage of covered bases [0..100]
meandepth	Mean depth of coverage
meanbaseq	Mean baseQ in covered region
meanmapq	Mean mapQ of selected reads

BLASTn output headers

Column header	Meaning
qseqid	Query sequence id
sseqid	Subject (matched allele) id
pident	Percentage of identical matches
length	Alignment length (sequence overlap)
mismatch	Number of mismatches
gapopen	Mumber of gap openings
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
qlen	Query sequence length
slen	Subject sequence length