Question: Filtering tblastn results
gravatar for juan.crescente
14 months ago by
juan.crescente40 wrote:

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:


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

ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 14 months ago by juan.crescente40

There 92% cover the 76 region.

ADD REPLYlink written 14 months ago by Medhat8.8k
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