samtools flagstat interpretation
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)
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asmaaaljuhani •
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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
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.
High percentage of aligned reads are also present in proper pairs in your alignment.
Hii, I got this result:
Please let me know if it is correct or not. What does it interpret?
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.
I am just asking about the result interpretation. I got your point.