Phred Score/Base quality score in Pysam

Question

[Lylthera]

Hi,

I'm examining the phred quality scores for bases of certain snps, so I wonder how to get this information - I'm using pysam and there's the method that provides quality scores (for example query_alignment_qualities or query_qualities).

In the doc it says, these are "aligned query sequence quality values (None if not present).", (or "read sequence base qualities", respectively). Does anybody know it these are phred scores, or if not, how would base quality else be computed in this implementation? Thanks in advance.

Answer 1

[glihm]

Hi Lylthera,

Yes, these are Phred scores. In the page 40 of this book you will find the confirmation. The Phred score is printed only for the aligned part.