qualimap bamqc results explanation

[kv]

Hi,

I recently found qualimap can be used for checking the quality of alignment. But I couldn't understand how the quality good or bad can be decided. Can anyone of you tell me something about my results.

Along with reads information I also see the following results. 

ACGT Content (inside of regions)
Number/percentage of A's  3,158,515,663 / 23.35%
Number/percentage of C's 3,553,930,924 / 26.28%
Number/percentage of T's 3,264,881,631 / 24.14%
Number/percentage of G's 3,548,438,496 / 26.23%
Number/percentage of N's 0 / 0%
GC Percentage 52.51%




Coverage (inside of regions)
Mean 101.97
Standard Deviation 2,079.74


Mapping Quality (inside of regions)
Mean Mapping Quality 3.48


Insert size (inside of regions)
Mean 10,890.82
Standard Deviation 573,320.48
P25/Median/P75 119 / 151 / 201

I see the mean mapping quality is 3.48. How to understand this? Can you also give me an idea about Coverage and GC percentage also whether this is good or not?

I'm also sending the images what qualimap produced. Could you please check that and tell me something about that. Please help me

Thank you

[Konstantin Okonechnikov]

Hi!

Some parameters are described in Qualimap documentation:

http://qualimap.bioinfo.cipf.es/doc_html/analysis.html#output

The detailed results interpretation depends on the experiment focus. For example, if the goal of project is mutation calling, then high coverage is expected across genome or in target regions. In general 100X is a good coverage for general tasks. GC content depends on species type, insert size on applied sequencing protocol/procedure, while mapping quality depends on the applied alignment tool. More details are also in SAM format description: https://samtools.github.io/hts-specs/SAMv1.pdf 

Best regards,

   Konstantin

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