samtools mpileup with
-s option, I get a 7th column with mapping quality. I realise the mapping quality in SAM format is calculated for a given read. I wonder what does a mapping quality mean for a single base position as it is the case in mpileup? Below is an example:
NW_008793873.1 12 A 1 . @ H NW_008793873.1 13 G 2 .^S. AB HS NW_008793873.1 14 A 2 .. @B HS NW_008793873.1 15 C 2 .. @B HS NW_008793873.1 16 g 2 .. BC HS NW_008793873.1 17 a 2 .. A@ HS
How can I interpret and use the mapping quality field for filtering bases?