Hello,

I want to filter my non-variant positions for mapping quality. I used mpileup to output the mapping qualities across all sites. To do the filtering, can I take an arithmetic mean of the mapping qualities for each read that the base belong to?

For example:

    NW_008793873.1 13 G 2 .^S. AB HS

Position 13 is covered by two reads with mapping qualities **H** and **S**. Would **(39 + 50)/2 = 44.5** be correct?

I ask this because in connection to mapping qualities, usually root mean square is mentioned so I was wondering what would the correct approach be in this case?

Thank you!
These are probabilities of mismapping on a PHRED scale. For the first one, the probability of mismapping is:

    (10^(-(39/10)) = 0.0001258925

For the second it is:

    10^(-(50/10)) =  1e-05

So on average, your probability of mismapping is:

    (0.0001258925+1e-05)/2 =  6.794627e-05

On a PHRED scale it is:

     -10*log10(6.794625e-05) =  41.67835

