I used samtools Flagstats walker. I am getting 0.0% properly paired reads in the BAM file. I sorted my BAM file and marked the duplicates as well. is there any BAM FLAG is missing in my file or mapping results are bad quality. Note that my average mapping quality (MAPQ) is more than 30.. i used bwa-mem for mapping to reference genome. i did not mark any duplicates in this step.
can you please help help me tracking this issue?
My command arguments were:
samtools flagstat /CHG000691/CHG000691_PE_02AL3.sam > /Flagstat/CHG000691/lanewise/CHG000691_PE_02AL3_flagstat.txt
75031887 + 0 in total (QC-passed reads + QC-failed reads)
733759 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
74460957 + 0 mapped (99.24%:-nan%)
74298128 + 0 paired in sequencing
37149064 + 0 read1
37149064 + 0 read2
0 + 0 properly paired (0.00%:-nan%)
73397388 + 0 with itself and mate mapped
329810 + 0 singletons (0.44%:-nan%)
2837608 + 0 with mate mapped to a different chr
982994 + 0 with mate mapped to a different chr (mapQ>=5)
Thank you very much!