I just performed a blastn, and I have some alignment returning qcovs = 0. I am not sure how this is possible because the alignment reports a pident and a bitscore for that alignment. For instance:
qseqid sseqid pident bitscore evalue qcovs qcovhsp length k127_1554010 ref|NZ_AONQ01000017.1| 77.007 409 2.85e-110 0 0
From my understanding, qcovs = query coverage. A qcovs = 0 means that 0% of the query is aligned to the subject. But why is the pident and bitscore reported as positive values?
Thank you in advanced!