Samtools Pileup Format

Question

[robles.daniela]

Dear all,

I hope you're well. I have a naive question about the samtools pileup format. The format looks like this:

http://samtools.sourceforge.net/pileup.shtml

My question is really what the 6th column is referring to. In that document (which is the official one), it says these are the base qualities encoded in ASCII format - 33. In this case, these then come from the sequencing machine used to perform the experiment. However, wikipedia says a different thing:

http://en.wikipedia.org/wiki/Pileup_format

In here, it says that this is the mapping quality of each of the bases. I have not heard of such a metric before but it might exist (as bases at the ends of a read probably map with poorer quality for example).

Any help in clearing this doubt would be greatly appreciated!

Thanks, Daniela

[Pierre Lindenbaum]

wikipedia doesn't say it anymore.

[robles.daniela]

Thanks very much Pierre. Than then settles it! :)

Answer 1

[Devon Ryan]

I changed the wikipedia page so it no longer reads "mapping quality" there, but rather "base quality".

Edit: Looks like someone (Pierre?) fixed the first 2 instances and I just fixed the 3rd.

[robles.daniela]

Yes, I see it now. Thanks for making everything clearer!