samtools flagstat interpretation- total value

Question

[deepthithomaskannan]

Hi all,

I got the flagstat output for my bam file as follows:

1639094206 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
1213460872 + 0 mapped (74.03%:-nan%)
1639094206 + 0 paired in sequencing
819547103 + 0 read1
819547103 + 0 read2
376403646 + 0 properly paired (22.96%:-nan%)
787827538 + 0 with itself and mate mapped
425633334 + 0 singletons (25.97%:-nan%)
382514288 + 0 with mate mapped to a different chr
75999056 + 0 with mate mapped to a different chr (mapQ>=5)

I got first(total) and second (mapped) values different. Does the first value is equal to the number of raw reads? I got the number of raw read info with me. But when I do the total number of raw reads I am getting a value which is lesser than the first value(1639094206). I am a little confused here. Any help appreciated.

Thanks,
Deepthi

Answer 1

[Pierre Lindenbaum]

your bam could contains some non-primary (flag= 256) or supplementary alignments (flag=2048) http://broadinstitute.github.io/picard/explain-flags.html = the number of alignments will be greater than the number of raw reads.