Different MAPPING QUALITY/PER-BASE QUALITY SCORE

[m_elena_bioinfo]

Hi NGS users,
someone could explain me the different between MAPPING QUALITY and PER-BASE QUALITY SCORE?

The score for the pileup is the Phred score of mapping quality?

I have a bit of confusion about it!
Thanx a lot
ME

[m_elena_bioinfo]

The mapping quality can be extracted from SAM or BAM file. But is there a way to do this using BIO:B::SAM modules?

To extract mapping quality using Bio:B::BAM, can I use:
$quality = $align->qual ?
It returns the quality score for the alignment as a whole.

[nilshomer]

Hi NGS users,
someone could explain me the different between MAPPING QUALITY and PER-BASE QUALITY SCORE?

The score for the pileup is the Phred score of mapping quality?

I have a bit of confusion about it!
Thanx a lot
ME

Read the supplementary materials in the Li et al. MAQ paper (Genome Research).