Samtools Pileup Format

Question

[Joanne Lim]

Hi,

What does "~" (tilde) and "]" means in column 5 (base string) of the samtools pileup format?

I cant seemed to find anything from here:- http://samtools.sourceforge.net/pileup.shtml

Thanks

Joanne

[Neilfws]

Can you give an example of that column? The meaning depends on where the character is in the string.

Answer 1

[Chris Miller]

I'm assuming that those characters are preceded by a ^, which means they represent the mapping quality. From the page you linked:

Also at the read base column, a symbol '^' marks the start of a read segment which is a contiguous subsequence on the read separated by `N/S/H' CIGAR operations. The ASCII of the character following '^' minus 33 gives the mapping quality.

[Neilfws]

That was my assumption too, hence my request for an example.

[Joanne Lim]

Hey,

Yes, that was what I meant. Actually I saw that in the example given in the link itself.

seq3 200 A 20 ,,,,,..,.-4CACC.-4CACC....,.,,.^~. ==<<<<<<<<<<<::<;2<<

So from this example "~" is the mapping quality followed by a match to the reference base, as seen from the "."? My bad, I've overlooked it.

Thanks!

[Chris Miller]

Glad it makes sense now, Joanne. If these answers were helpful to you, don't forget to upvote and choose a best answer by clicking the checkbox next to it. Welcome to BioStar!

[Joanne Lim]

Hey! Many thanks for your input and patience :). Another question though, which reads is the mapping quality referring to (just to confirm)? In my case:-

,,,,,..,.-4CACC.-4CACC....,.,,.^~.

does the (~) infer the mapping quality of the entire reads succeeding the "^" sign? In here its the mapping quality of the "." ?

Sorry for the primitive questions,appreciate your insights!

[Chris Miller]

I believe that it's just the quality of the read starting at that position that is associated with the immediately subsequent base.

[Chris Miller]

I believe that it's just the quality of the read starting at that position (with the immediately subsequent base)