Doubt samtools flagstat
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)
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I'd start by examining why the properly paired % is so low.
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.shfrom BBMap in that case.I am comparing a variant of the ITS region that is not very common.