Per base sequence quality and per base N content

[barthez95]

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.

[GenoMax]

FastQC uses varying levels of data sampling (due to time/memory constraints) to do various tests it presents. It is possible that could be the reason for the discrepancy you are noticing.