meaning of new symbols in samtools mpileup format?

Question

[Dejian]

Samtools v1 is released. I found some new symbols in the samtools mpileup results. The command I used is samtools mpileup -l $snpPos -f $REFfa -sO -o res.mpileup samp.bam. In the 5th column of the result file, some new symbols appeared (see symbols = and ~ below). These are two examples of part of the long string:

.....T...........^$.^$.^$.^".^$.^".^$.^".
T.TTTT....TT...TT,,......,^~.^~.^~.^~.^~.

For most symbols, they are explained before. But what are the meaning of the new symbols colored in yellow? Is there a document mentioning these changes? Thanks!

[Devon Ryan]

If it's possible that you have MAPQs of 93 (~ minus 33) then these would be reasonable. Otherwise, something does seem off.

[Dejian]

Sorry, Devon, I still don't quite understand what you mean. The 5th column of pileup output is read bases and the 6th column is base qualities. It seems that it is not related to MAPQ. Did you take it for a question about sam format (5th column is MAPQ)?

Answer 1

[Devon Ryan]

N.B., I moved this comment to an answer so others don't click through thinking this issue still needs addressing.

No, I didn't take it for a question about SAM files. The 5th column of the pileup format always also included MAPQ scores when an alignment starts (denoted by ^ followed by MAPQ+33). This is also mentioned in the link in your post (note the penultimate paragraph). Having said that, a MAPQ of '=' makes a bit more sense than '~', but perhaps your aligner outputs MAPQs that high.

[Dejian]

You are right. Thanks a lot.