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Old 03-02-2016, 01:03 AM   #1
Location: ireland

Join Date: Apr 2014
Posts: 18
Default MAPping Quality v.s. Alignment Score (AS) in SAM format

MAPQ: MAPping Quality. It equals −10 log10 Pr{mapping position is wrong}, rounded to the nearest
integer. A value 255 indicates that the mapping quality is not available.

AS i Alignment score generated by aligner

What are the differences between these two? I am confused about this. If I want to filter the alignments and keep the 'good' alignment, which value should I look into?

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