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 i done mistake and how can fix this problem.
Thanks in advance