Samtools Pileup Format
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9.6 years ago
Joanne Lim ▴ 20

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

pileup format samtools • 4.5k views
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Can you give an example of that column? The meaning depends on where the character is in the string.

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9.6 years ago

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.

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

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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!

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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!

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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!

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

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

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