What Does Qc-Passed/Failed Reads Mean In Samtools Flagstat?

Question

[KJ Lim]

8075928 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
4723128 + 0 mapped (58.48%:nan%)
8075928 + 0 paired in sequencing
4037964 + 0 read1
4037964 + 0 read2
1370328 + 0 properly paired (16.97%:nan%)
1370328 + 0 with itself and mate mapped
3352800 + 0 singletons (41.52%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

This is the flagstat result I obtained from paired-end mapped BAM file with SRHiMP2.The total paired-end reads are 114 100 948 but only 8 075 928 reads shown in the flagstat.

Could anyone kindly lights me how the QC-passed/failed reads come to?

Thanks a lot. Have a nice day.

Answer 1

[Istvan Albert]

In the SAM specification flag 0x200 (512) stands for "not passing quality controls". This is a platform/aligner specific flag that does not have a unique definition.

I believe that the flagstat output counts these flags. Most aligners that I have seen do not actually make use of this flag so most of the time this value is not relevant.

[Lim]

Thanks for your prompt replied, Istvan.

[Zev.Kronenberg]

There are several mysterious flags in BAMs

Answer 2

[Lim]

I'm confuse with the flagstat result of BAM file.

The total paired-end reads are 114 100 948 but only 8 075 928 reads were reported mapped. How could I find the related information for the other 106 025 020 reads or what happen to these reads?

Thanks for the time and help.