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Old 05-21-2018, 01:31 PM   #1
barthez95
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Location: Linux

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Default Per base sequence quality and per base N content

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.
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File Type: png Screen Shot 2018-05-21 at 23.28.57.png (17.0 KB, 6 views)
File Type: png Screen Shot 2018-05-21 at 23.29.14.png (11.9 KB, 6 views)
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Old 05-22-2018, 09:35 AM   #2
GenoMax
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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.
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