Question: samtools flagstat interpretation
0
gravatar for asmaaaljuhani
10 months ago by
asmaaaljuhani0 wrote:

How can I interpret the following results? and is there a specific percentage that we accept the allignment?

samtools flagstat aln-pe.sam 

13167602 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 secondary

0 + 0 supplementary

0 + 0 duplicates

12146736 + 0 mapped (92.25% : N/A)

13167602 + 0 paired in sequencing

6583801 + 0 read1

6583801 + 0 read2

11736544 + 0 properly paired (89.13% : N/A)

11905248 + 0 with itself and mate mapped

241488 + 0 singletons (1.83% : N/A)

113814 + 0 with mate mapped to a different chr

23958 + 0 with mate mapped to a different chr (mapQ>=5)
samtools flagstat • 429 views
ADD COMMENTlink modified 10 months ago by ATpoint36k • written 10 months ago by asmaaaljuhani0

Hi, please add details on what data you are showing here: [ Please read before posting a question ] -- How To Ask A Good Question

ADD REPLYlink written 10 months ago by ATpoint36k

is there a specific percentage that we accept the allignment?

There are no hard and fast rules about that. It is partially dependent on what you are comfortable with and what kind of an experiment you are working with. Alignments in 90+% range are great.

12146736 + 0 mapped (92.25% : N/A)

High percentage of aligned reads are also present in proper pairs in your alignment.

11736544 + 0 properly paired (89.13% : N/A)

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax87k
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