Entering edit mode
21 months ago
igorm
▴
20
Hi,
I am trying to understand the samtools mpileup bases string output and I am having problems with:
- ^ (caret) marks the start of a read segment and the ASCII of the character following `^' minus 33 gives the mapping quality
- $ (dollar) marks the end of a read segment
Example
1 10001 T 16 ,..^!.^I.^!.^!.^..^!.^!.^!.^!.^!.^0.^".^!.
The fourth element of the string is ^, which annotates the starts of the read segment. But to which read does this refer to? Does is refer to the read before the ^ - third element of the string (which is . therefore T) or to the read after !?
Thanks!