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?
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?