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Meaning of MQ value

MennoMenno United KingdomMember

Dear GATK team,

I am wondering: is there an easy way to interpret the MQ value?
I know that MQ stands for the 'root mean square (RMS) of Mapping Quality', and that it gives 'an estimation of the overall mapping quality of reads supporting a variant call'.
But is there a kind of relation, similar to a Phred score, between the observed MQ value and the probability that the variant call is erroneous?
I am asking because I wonder which MQ values to consider acceptable. (I am aware that the GATK webpage (http://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set) suggest a MQ-threshold of 40.)

Thanks a lot in advance for your response.

All the best,

Menno de Jong


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