mapping quality

[Wuxy96]

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.

[fritzsedlazeck]

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