Hi,
I am using SAMTOOLS MPILEUP and I have trouble understanding the output.
What I know is:
-> output
- Sequence name
- 1-based coordinate
- Reference base
- Number of reads covering this position
- Read bases
- Base qualities
Alignment mapping qualities
. -> match to the reference base on the positive strand
, -> match to the reference base on the negative strand
lowercase letter -> indicates a mismatch was on a read that mapped on the negative strand
uppercase letter -> indicates a mismatch was on a read that mapped on the positive strand
So far-so good. What I don't understand is if there is a way to know, for each position, what exactly I got, since I am getting some symbols like ^~ or -2aa Can you point me to somewhere where all possible characters are explained?