What Does A "*" (Star) Mean In Mpileup'S "Read Bases" Column (The 5Th Column)?

Question

[Panos]

I checked the documentation but can't find its meaning.

Answer 1

[Russh]

It's the shadow of a deletion.

Suppose you have the following as refereence

ACGTCGCTCGCTCG

and the following is your sequence of interest, relative to the reference

ACGAC--TGGCTCG

Let's say you received the read ACGACTGG from some sequencing data. This read overlaps the deletion in your sequence of interest.

So, positions 6 and 7 are deleted in your sequence of interest relative to the reference, and so aren't in your sequence read, but are covered by that read. These positions are given *s in the mpileup

Relative to the 1-based ref coordinates, in your mpileup:

4->A 5->. 6->* 7->* 8->. 9->G

HTH, Russ (who does hope they get called deletion shadows if the docs get updated..)