Why Is A Base Quality Score Associated With A Base Deletion In A Pileup File?

Question

[Anjan]

Hi, It turns out that a pileup generated from a .bam file, by samtools (option mpileup), assigns a base quality score to a base deletion. In the example below there is a G deleted from position 53 in a read aligning to the phiX sequence. This is indicated by a "" in the pileup at line 53. This "" seems to have a base quality score of 13.

phix174    134    T    52    ............................................,.......-1G    ABF=B8EC4FD;BFFDFDHFHHGFH=DFHHEH=HIAIFFIEFCACAGD5@D-
phix174    135    G    53    ............................................,......*^].    CCCBE8FE;EE;EEHFF=HFHHHGF=HHHHBH?FGFIBGHE;..CAGG5@D.?

How is it possible for a deletion to be assigned a "base" quality score? Thanks, Anjan

[Gabriel R.]

just to be sure, what version of samtools are you using ?

Answer 1

[fo3c]

That's not the case. Indels are reported together with the previous base, so there is a match with score 13, and right after that match there is an indel without quality score.

It's clearer this way:

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . , . . . . . . .-1G
A B F = B 8 E C 4 F D ; B F F D F D H F H H G F H = D F H H E H = H I A I F F I E F C A C A G D 5 @ D -