Question: BLAST qcov equals to 0
gravatar for Ming
16 months ago by
Ming50 wrote:

Hello All,

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!

blast • 395 views
ADD COMMENTlink modified 14 months ago by h.mon30k • written 16 months ago by Ming50

Can you provide the parameters that you have defined for your blast?

ADD REPLYlink written 14 months ago by mgdias.jose10

that output is not corresponding to the header you provide, length has no value (from the top of my head, I even think 'length' is not a valid field)

can you provide your actual blast command (as also mgdias.jose requested)

ADD REPLYlink modified 14 months ago • written 14 months ago by lieven.sterck8.3k
gravatar for h.mon
14 months ago by
h.mon30k wrote:

As lieven.sterck noted above, the output does not correspond to the header - which may indicate you did something wrong / the output fields are not exactly what you think they are.

I will have an attempt at another (rather wild) guess:

The name of your query and subject indicates you are blasting MEGAHIT contigs against bacterial genomes - potentially very long sequences. If you have a strong short similarity, blast will output the hit, but qcov may be set to zero because it is a tiny fraction of a percentage. Try to use qstart, qend, sstart and send to see how long are the alignments.

ADD COMMENTlink written 14 months ago by h.mon30k
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