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Old 03-16-2012, 01:38 PM   #1
Location: New York, NY

Join Date: Oct 2011
Posts: 41
Default BWA aligned pairs read1=XT:A:U, read2=XT:A:R


I've aligned Illumina paired end reads with BWA, filtered using samtools view -f 3 -F 12 ("proper pairs", both mates mapped).

I'm looking at the XT tags and see expected classes, where both mates are XT:A:U (both "unique") and XT:A:M + XT:A:U (one mate-rescued, one "unique").

However, I also find a class of paired reads where one read is XT:A:R (multiply-mapped) and the other is XT:A:U. This class of reads is a significant fraction of the total pairs (~10%) and the class persists after filtering on MAPQ > 20.

I anticipated that this class of reads would instead be classifed in the XT:A:M + XT:A:U (ie XT:A:R converted to XT:A:M), but apparently not.

Are the XT:A:R whose mate is XT:A:U mate-rescued, or something else?

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Old 07-29-2014, 10:06 PM   #2
Location: Japan

Join Date: Jul 2010
Posts: 11

I have exactly the same question and I haven't been able to find more detailed information on the XT:A:M tag from BWA.

I created a simple example (on my blog at; specifically the "RESCUING AMBIGUOUSLY MAPPED READS" section) trying to obtain the XT:A:M tag by aligning a uniquely- and multi-mapping pair but I got the XT:A:U and XT:A:R tags instead.

Last edited by davetang; 09-09-2014 at 02:41 AM. Reason: Removed the semi-colon from the URL.
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