Hello,
Can anyone provide a clear definition of what exactly the BLAST+ output parameters 'qcovs' and 'qcovhsp' are? From the help pages:
"qcovs means Query Coverage Per Subject"
"qcovhsp means Query Coverage Per HSP"
But beyond this I'm less sure. My interpretation of this is that qcovs is the query coverage summed over all potential HSPs, but does this simply sum over HSPs or does it account for the possibility of overlap among HSP alignments? I guess the first case could result in coverages of > 100%, whereas the latter would be more appropriate (and more useful). My interpretation of qcovhsp is that this returns a coverage value that is specific to each individual HSP, but are these returned one per line, or are they delimited in some way?
I've Googled around and looked up the BLAST documentation but couldn't find much, apologies if I've missed something obvious.
Cheers.