Question: Per base sequence quality and per base N content
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gravatar for bwczech
4 weeks ago by
bwczech0
bwczech0 wrote:

Hi, I have one incomprehensibleness with my FastQC's report. Usually N's have quality=2, so if our N content in e.g 99bp = 35% we should observe these on the first plot.

I attached printscreens from my FastQC and I have a question:

if on 99bp N's content >30%, and quality of N =2, why I cannot notice fewer value of lower whisker on the 1st plot? These N's should underestimate quality value in these position. enter image description here

enter image description here

fastqc quality • 120 views
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