Hello group,

I am trying to get the percentage of reads mapped to refernce using samtools. I used the command samtools flagstat sequence.bam, but the result I am getting is bit worst than I was expecting, as it shows only 34% of reads mapped.

438974667 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
151842378 + 0 mapped (34.59%:-nan%)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (-nan%:-nan%)
0 + 0 with itself and mate mapped
0 + 0 singletons (-nan%:-nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

I wanted to know why I am getting this result, and where have done mistake and how can fix this problem.

Thanks in advance