Blast qcovs column misleading
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14 months ago
mitchez ▴ 20

Hi, I am trying to figure out how blastn calculates the values noted in the column qocvs

Here is my example:

qseqid         sseqid  sstart    send  pident qcovs qlen length mismatch gapopen gaps evalue bitscore
full refNZ_CP033688  352587  353830 100.000   100 2423   1244        0       0    0      0     2298

According to blastn qcovs is 100 but (length/qlen)*100 = 51%

Does anyone have an explanation for that calculation?

blast • 221 views
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