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Published 20 hours ago • verified publisher icon philres

mapping quality

Open Wuxy96 opened this issue 4 years ago • 1 comments

Hi, May I know the formula of mapping quality in sam. I wonder how to calculate this value, and the threshold of high mapping quality. Thanks.

Wuxy96 avatar Apr 21 '20 07:04 Wuxy96

Every mapper does it slightly differently. It is basically representing the edit distance between the first and 2nd best alignment of a read. There is greater detail in the SAM documentation I think.

https://genome.sph.umich.edu/wiki/Mapping_Quality_Scores

Typical thresholds are either 10+ or 20+ depending on how much you want to filter. For NGM MQ=0 is saying that its not a unique mapping read. MQ1-5 says its unique mapping but there might be a 2nd alignment that is just different by 1-2 bp.

Hope that helps Fritz

fritzsedlazeck avatar Apr 21 '20 14:04 fritzsedlazeck