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!