Question: What Does Qc-Passed/Failed Reads Mean In Samtools Flagstat?
1
gravatar for KJ Lim
6.8 years ago by
KJ Lim120
KJ Lim120 wrote:
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.

samtools qc • 7.1k views
ADD COMMENTlink written 6.8 years ago by KJ Lim120
2
gravatar for Istvan Albert
6.8 years ago by
Istvan Albert ♦♦ 77k
University Park, USA
Istvan Albert ♦♦ 77k wrote:

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.

ADD COMMENTlink written 6.8 years ago by Istvan Albert ♦♦ 77k

Thanks for your prompt replied, Istvan.

ADD REPLYlink written 6.8 years ago by Lim0

There are several mysterious flags in BAMs

ADD REPLYlink written 6.6 years ago by Zev.Kronenberg11k
0
gravatar for Lim
6.8 years ago by
Lim0
Lim0 wrote:

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.

ADD COMMENTlink written 6.8 years ago by Lim0
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