How can "samtools flagstat" report an odd number of reads "with itself and mate mapped"? I don't get that...
samtools flagstat reads.bam
Any idea?
Reads come from a mate pair protocol, sequenced on HiSeq, aligned by bwa.
Thanks!
samtools flagstat reads.bam
Code:
161533046 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 duplicates 137350248 + 0 mapped (85.03%:-nan%) 161533046 + 0 paired in sequencing 80766523 + 0 read1 80766523 + 0 read2 106075436 + 0 properly paired (65.67%:-nan%) 124869771 + 0 with itself and mate mapped 12480477 + 0 singletons (7.73%:-nan%) 8181512 + 0 with mate mapped to a different chr 4410235 + 0 with mate mapped to a different chr (mapQ>=5)
Reads come from a mate pair protocol, sequenced on HiSeq, aligned by bwa.
Thanks!