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

[asheenlevrai]

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-

[asheenlevrai]

Anyone has an idea how reads with XA tags can have a mapping quality >0?

These reads also have XT = U, meaning they should be unique, right? how can reads have XT=U and multiple XA tags???

[Jim Robinson]

Hi, this is probably a question best addressed by the developers of the aligner you are using, is it BWA? mq == 0 means that a read had multiple equally good placements. The definition of the XA tag is "alternative hits", it doesn't say, necessarily, equally good quality hits.

The most authoritative place to get an answer on this is the BWA forum, hopefully Heng himself will weigh in (bio-bwa-help). If you do get an answer please post it here as well.

Jim

[asheenlevrai]

I was using BWA via the galaxy project website