samtools flagstat interpretation
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21 months ago

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

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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)

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Hii, I got this result:

20219926 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
91746 + 0 mapped (0.45% : N/A)
20219926 + 0 paired in sequencing
10109963 + 0 read1
10109963 + 0 read2
20252 + 0 properly paired (0.10% : N/A)
28096 + 0 with itself and mate mapped
63650 + 0 singletons (0.31% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)

Please let me know if it is correct or not. What does it interpret?

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I told you already in the other thread that there is nothing we can do from remote. You have poor alignment, why that is needs to be investigated by you and the people producing the library. Apparently it is not adapter content as discussed already. You have 0.45% of reads aligning, that is troublesome, something is wrong, either library or a wrong reference genome, can be basically anything.

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I am just asking about the result interpretation. I got your point.

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