BWA dbwtsw to Samtools Pileup - what is the score?

[aldrinyim]

Hi everyone I am using Samtools pileup after doing a bwa-dbwtsw alignment. The output came in this way

Contig 884 T T 229 0 25 67 ....,,,,.,.,,.,,,.,,,,.,,....,,,.,..,.,,.
,.,..,....,,,..,,,,,,,..., =@@<EI???DE??F?=DA?FFFDDFDD?D?EEAF?@?D?F7??EFICIIEI@A@>DA@@@@@CF>;?

Correct me if i am mistaken, I guess 229 should be the score? What is the scoring system? How should I interpret this score?

thanks!

[zeynep]

Hello,
I believe this link would be helpful to you.

http://sourceforge.net/apps/mediawik..._pileup_output.

[aldrinyim]

Thanks for the website but what actually is a "Phred-scaled likelihood"?
Moreover, if the data are generated by solexa, the "Phred-scaled likelihood" would not jump up to 200 something, so that's why I am kind of curious with this.

So I suppose the higher the score, the better the basepair quality?