contradictory or not?

[Layla]

Hi

I have spotted the following after a maq map command on paired end:
Base qualities of a read to be QSolexa -2.3 (i.e. very poor) , but assigned a flag of 18 (correct pair) and a mapping quality of 95 (suggesting the alignment to the genome reliable).

Is this logical and correct?

Any input would be appreciated

Cheers
L

[johar]

This indicates that the alignment works independently of the quality value and when alignment is fine the score is higher irrespective of the quality. You can take care of it if you filter out low quality reads if necessary and unwanted.

[Layla]

Thought so

Hmm, makes sense. Thanx