samtools flagstat ?

[yuntwang]

Hi,
Recent I use minimap2 deal with the nanopore data and get the final bam.
I want to get the mapping ratio and use the samtools flagstat to get the result.
And find a question: my total reads in nanopore is about 810801.
But the samtools flagstat:
1243932 + 0 in total (QC-passed reads + QC-failed reads)
345546 + 0 secondary
87585 + 0 supplementary
0 + 0 duplicates
1229053 + 0 mapped (98.80% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
The total reads is about 1243932!
Why?
Hope to get your reply.
Thanks

[lh3]

Caused by supplementary alignments. This is really a samtools question.

[yuntwang]

Hi,@lh3
Can I use it as a true mapping ratio?
if not, any other statistical software for the minimap2?

Thanks.

[rebeelouise]

Hi,@lh3
Can I use it as a true mapping ratio?
if not, any other statistical software for the minimap2?

Thanks.

Did you ever resolve this?