I'm using "qcovus" in my blast command in order to to retrieve only unique hits between two sequences (no overlap):
blastn -query q.fa -subject s.fa -outfmt "6 std qlen slen qcovs qcovus"
I'm getting a strange behavior..
q.fa and s.fa are single node genomes, with very similar length (<1% difference).
When I blast in one direction (a->b), I get: qcovs=96% and qcovus=96% When I blast the other way around (b->a), I get: qcovs=96% and qcovus=60%
This surprises me, I looked for some bug in the beginning, but everything seems to be working correctly. I dare not suggest Blast has a bug either. Can anyone explain what might be happening here?