The following is the output of samtools flagstat command on bam file (paired-end) generated after markDuplicate of Picards.
7417232 + 0 in total (QC-passed reads + QC-failed reads)
287618 + 0 duplicates
4534962 + 0 mapped (61.14%:-nan%)
7417232 + 0 paired in sequencing
3708616 + 0 read1
3708616 + 0 read2
4528278 + 0 properly paired (61.05%:-nan%)
4534962 + 0 with itself and mate mapped
I am having difficulty in understanding whether the duplicates are pairs or single. If there are total of 7417232 pairs and out of them 287618 pairs are duplicates means, there are 3% of duplicate reads in my data. Is my understanding is correct ?