Allele-specific root-mean-square of the mapping quality of reads across all samples (AS_MQ)
This annotation provides an estimation of the mapping quality of reads supporting each alternate allele in a variant call. Depending on the tool it is called from, it produces either raw data (sum of squared MQs) or the calculated root mean square.The raw data is used to accurately calculate the root mean square when combining more than one sample.
The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.
Uninformative reads are not used in this annotation.
GATK version 126.96.36.199 built at Wed, 30 Jan 2019 10:21:04 +0530.