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samtools flagstat result is different from samtools view result

Hi All. I wonder if anyone of you have inconsistent mapping result generated by samtools flagstat and samtools view command?

My samtools flagstat output is as below:

3217 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
2788 + 0 mapped (86.66%:nan%)
393 + 0 read1
393 + 0 read2
480 + 0 properly paired (61.07%:nan%)
480 + 0 with itself and mate mapped
148 + 0 singletons (18.83%:nan%)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

The total mapped reads number is 2788. However, when I did samtools view and do a read count on those mapped to reference, the number was 2936. I wonder why the number is different in this case.

samtools
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updated by macielrodriguez2 • macielrodriguez2 • written by Louis Kok • Louis Kok 
> 3217 + 0 in total (QC-passed reads + QC-failed reads)

What represents the number 3217? The total number of reads analized?

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written by macielrodriguez2 • macielrodriguez2

What you mean by analyzed? It means in this file there are 3217 reads.

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written by ATpoint ATpoint

Sorry for the mistake and thank you for the answer. I was a little confused with my own results of flagstat:

6060680 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
6051340 + 0 mapped (99.85%:-nan%)
6060680 + 0 paired in sequencing
3032920 + 0 read1
3027760 + 0 read2
5669320 + 0 properly paired (93.54%:-nan%)
6042000 + 0 with itself and mate mapped
9340 + 0 singletons (0.15%:-nan%)
257886 + 0 with mate mapped to a different chr
28511 + 0 with mate mapped to a different chr (mapQ>=5)
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written by macielrodriguez2 • macielrodriguez2

1 answer

samtools flagstat splits out the reads which mapped as a pair (2,788) vs those which mapped only as singletons (148).

2,788 + 148 = 2,936.

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written by Dan D Dan D

Thanks Dan for the explanation. For the number of reads mapped, would you take in consideration of singletons as well?

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written by Louis Kok • Louis Kok

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