Why does mpileup tell me the starting and ending base of a read?

Question

[Peavil]

Mpileup tells the start and end base with $ or ^.

   chr1 1374834 A   19  gggGgggGggggGgggGg^Sg   ===95=>9>=?:8@@@859
   chr1 1551927 T   32  .$..,,,,..,..,..,...,,,,...,,....   I34>>=>1>==9>69><<<=??;<<<?A;;>=

I wonder what these things mean.

• Why is it telling me the start and end base of a read?
• Why does it tell me the mapping quality of the only start-base, not end-base?

Answer 1

[Vasisht]

The mapping quality is for the entire read and not just a particular base. mpileup can also output the mapping qualities of the read covering each base with the -s option and the base positions with the -O option. The start and end positions are special cases, where if coverage of a particular base is mostly at the start or at the end, that could potentially imply some bias.