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Here is my flagstat output after running bwa mem on my paired end data.
25730940 + 0 in total (QC-passed reads + QC-failed reads)
111474 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
25300974 + 0 mapped (98.33% : N/A)
25619466 + 0 paired in sequencing
12809733 + 0 read1
12809733 + 0 read2
24045298 + 0 properly paired (93.86% : N/A)
25182938 + 0 with itself and mate mapped
6562 + 0 singletons (0.03% : N/A)
1071166 + 0 with mate mapped to a different chr
297377 + 0 with mate mapped to a different chr (mapQ>=5)
So from my understanding, 93.86% of my reads are properly paired which means the read and its mate mapped with decent distance to the same chromosome. So does "with itself and mate mapped" simply mean that both reads did map but maybe not all of them are within good distance from each other? Does it also mean both did map to the same chromosome? It is unclear to me what that category means but it does make sense to me that the number of reads would be higher.
25730940 + 0 in total (QC-passed reads + QC-failed reads)
111474 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
25300974 + 0 mapped (98.33% : N/A)
25619466 + 0 paired in sequencing
12809733 + 0 read1
12809733 + 0 read2
24045298 + 0 properly paired (93.86% : N/A)
25182938 + 0 with itself and mate mapped
6562 + 0 singletons (0.03% : N/A)
1071166 + 0 with mate mapped to a different chr
297377 + 0 with mate mapped to a different chr (mapQ>=5)
So from my understanding, 93.86% of my reads are properly paired which means the read and its mate mapped with decent distance to the same chromosome. So does "with itself and mate mapped" simply mean that both reads did map but maybe not all of them are within good distance from each other? Does it also mean both did map to the same chromosome? It is unclear to me what that category means but it does make sense to me that the number of reads would be higher.