why the properly paired results from bwa mem is an odd number

[Pengfei Liu]

Hi
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?

thanks!

[lh3]

That is because of chimeric alignment.

[Pengfei Liu]

Thanks for your reply!