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Old 08-22-2013, 07:25 PM   #1
Pengfei Liu
Location: Beijing

Join Date: Nov 2012
Posts: 16
Question why the properly paired results from bwa mem is an odd number

following is the results of samtools flagstat results. I use bwa mem default command to do align! my question is why the properly paired is odd number?

25700926 mapped

25744459 + paired in sequencing

12897523 read1

12846936 read2

25445603 properly paired

25692729 with itself and mate mapped

8197 singletons

my reads are from a archaea RNA-seq experiment.

and how to get unique mapped read-pairs from the properly paired?

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Old 08-23-2013, 10:42 AM   #2
Senior Member
Location: Boston

Join Date: Feb 2008
Posts: 693

That is because of chimeric alignment.
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Old 08-24-2013, 07:26 PM   #3
Pengfei Liu
Location: Beijing

Join Date: Nov 2012
Posts: 16

Thanks for your reply!
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odd number, properly paired

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