I have a protein sequence of a gene of interest I got from uniprot. I also have the full genomic sequences of my plant. I want to map where the gene is or if there are multiple copies. Since tblastn does not have many filtering options I started to manually filtering the best hits with high % of identity.
tblastn -evalue 1e-10 -query gene.fa -subject genome.fna -outfmt "6 qseqid sseqid qstart qend sstart send mismatch gaps pident evalue length qlen slen qcovs score"
But interestingly the qcovs looks odd, for example one of the results is as follow:
length:76 qlen:545 slen:65861 qcovs:92
How is the query coverage 92% if the length of the alignment is only 76nt and the query length is 545? I struggle to find any information in blast documentation that cover this subject