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.