Hi,

I am using SAMTOOLS MPILEUP and I have trouble understanding the output.

What I know is:

-> output

1. Sequence name
2. 1-based coordinate
3. Reference base
4. Number of reads covering this position
5. Read bases
6. Base qualities

7. 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?