Mapping Quality vs. XA tag (I'm lost)

[asheen...@hotmail.com]

Hello all,

In IGV, reads with a mapping quality = 0 are displayed in white while reads with a positive mapping quality are displayed in grey (at least for the bam file I am trying to analyze).

From what I could deduce from the information displayed when I hover over a read, I thought that white reads would be the ones mapping at several locations on the reference genome while grey reads would be the ones with a unique mapping location. However, I just found some grey reads with XA tags, which in my case, mean that they map to 3 different locations on the genome...

AAAAAAAArrrgh!!

I don't understand what I'm doing, I guess...

Could anyone explain to an idiot like me, how this works? What is the mapping quality then? How can I determine which are the reads with a unique target in the genome?

Thank you very much in advance for your help
-a-

[Jim Robinson]

Hi,

This is probably a question best posted to SeqAnswers but I will give it a shot.   The interpretation of mapping quality is somewhat dependent on the software that aligned it,  I suppose, but my understanding is it means the read could not be uniquely placed.   That does the question of what non-zero mapping quality reads with multiple mappings mean.    I will do some investigation, but if you post on SeqAnswers please include "IGV" in the subject line and I will follow that as well.

BTW, with the "early access"  IGV you can color alignments by any arbitrary tag,  so selecting "Color alignments by tag" and entering XA might give you a better view of this.

-- Jim