Doubt samtools flagstat

Question

[Etienne]

I'd like to see the percentage of how many sequences align with my decrementing sequence and I've come to this sample table. But wanted to know what use? The mapped (80.94% : N/A)or properly paired (0.06% : N/A) percentage?

1036193 + 0 in total (QC-passed reads + QC-failed reads)
197709 + 0 primary
0 + 0 secondary
838484 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
838710 + 0 mapped (80.94% : N/A)
226 + 0 primary mapped (0.11% : N/A)
197709 + 0 paired in sequencing
89047 + 0 read1
108662 + 0 read2
124 + 0 properly paired (0.06% : N/A)
226 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

[swbarnes2]

I'd start by examining why the properly paired % is so low.

[GenoMax]

Since 80% of reads are mapped it is likely that the reads are out of sync if the R1/R2 files were processed/trimmed independently. Fix using repair.sh from BBMap in that case.

[Etienne]

I am comparing a variant of the ITS region that is not very common.