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
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
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