Strange looking Interactive quality plot

[Nicholas_Bokulich]

Hi @Trodgers ,
Nothing to worry about, this is because the data were generated using NextSeq. See here for more details:

Strange Interactive Quality Plot after Importing the data

Hi @ari_sh70, The quality scores of the newest generations of Illumina machines (including NovaSeq in your case) use a new more "streamlined" binning system for quality scores which does not give the traditional continuous Phred scores you may be familiar with, rather it bins the values into 4 values only, thus the very artificial looking quality plots you see. But this is totally expected. Now, how these newer binning systems affect the downstream quality control/denoising is a different discu…