HI,

I am trying calculate RMS (root-mean-square) MQ (MappingQuality) from a bam file for ever sites (even no variation), I visited GATK's blog:

https://gatk.broadinstitute.org/hc/en-us/articles/360037591751-RMSMappingQuality

I note they said:

Overview

Root Mean Square of the mapping quality of reads across all samples. This annotation provides an estimation of the overall mapping quality of reads supporting a variant call, averaged over all samples in a cohort.

The raw data format for this annotation consists of a list of two entries: the sum of the squared mapping qualities and the number of reads across variant (not homRef) genotypes

So if I want to calculate a RMSMQ for no variation site (homRef), can I use following formula?

RMS_MQ = sqrt(sum(MQ_i^2)/N)      .......... (1)

where, MQ_i is the MQ of reads i coverage the site, N is the total number of reads coverage the site.

If this is correct, I note this section in GATK:

Statistical notes The root mean square is equivalent to the mean of the mapping qualities plus the standard deviation of the mapping qualities.

Its means:

RMS_MQ = mean(MQ_i) + sd(MQ_i)     ........... (2)

Is it correct? but I noted the output of formula (2) is not equal to formula (1)