Re: [Samtools-help] SAMtools pileup format

[Sean D. <sd...@ma...>]

Those mark the beginning of reads and the associated mapping quality.
See the second-to-last paragraph of the page you reference for
details.

Sean


On Mon, Jun 27, 2011 at 11:19 AM, dong he <don...@gm...> wrote:
> Hi,
>
> Does anybody can tell me where I can find the detail explanation of
> pileup format? by reading the manual from
> http://samtools.sourceforge.net/pileup.shtml, I still don't understand
> some symbols such as ^~, ^l, ^k, ^+.....
>
> --------------------------
> seq1 1 C 1 ^~. <
> seq1 2 A 1 . <
> seq1 3 C 2 .^~. <<
> seq1 4 T 2 .. <<
> seq1 5 A 3 ..^~. <<<
> seq1 6 G 4 ...^`. <<<(
> seq1 7 T 4 .... <<<-
> seq1 8 G 4 .... <<<&
> seq1 9 G 5 ....^~. <<<-<
> seq1 10 C 5 ..... <<<-<
> seq1 11 T 5 ..... <<<-<
> seq1 12 C 5 ..... <<<-<
> seq1 13 A 7 .....^~.^~. <0<,<<<
> seq1 14 T 7 ....... <<<-<<<
> seq1 15 T 8 .......^~. <<<-<<<<
> seq1 16 G 8 ........ ;<7-<<<<
> seq1 17 T 8 ........ <<;-<<<<
> seq1 18 A 9 ........^l, <67)<<;<=
> -------------------------------
>
>
> Thanks
>
> Dong
>
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