I have a rookie question. I was using the
samtools flagstat to check the statistics of bam files. When I view the results of that bam file, I see that number of reads which pass the QC is sometimes more than the number of reads which mapped. My understanding is that bam files only include mapped reads. Does it have unmapped reads too?
An e.g., is:
$ samtools flagstat file.bam 257823892 + 0 in total (QC-passed reads + QC-failed reads) 132531248 + 0 duplicates 209402202 + 0 mapped (81.22%:nan%) 257823892 + 0 paired in sequencing 128911946 + 0 read1 128911946 + 0 read2 152678438 + 0 properly paired (59.22%:nan%) 48421690 + 0 singletons (18.78%:nan%) 3565988 + 0 with mate mapped to a different chr 1316058 + 0 with mate mapped to a different chr (mapQ>=5)
Here, the mapping is 81.22%. I thought if the bam files have only mapped reads, then it should be 100% mapped. Can anyone help me understand this? Tried looking online but no luck.
The bam file was generated by Lifescope mapping using paired SOLiD reads.