Strange looking Interactive quality plot

[Trodgers (Torrey Rodgers)]

Hello,
I recently got some data back from a NextSeq run, and the quality plot looks really strange, and I am loosing a lot of the data (around 75%) when running DADA2, mostly at the chimera removal step. I did a little pilot run on MiSeq, and the data turned out good, but our sequencing center just got the NextSeq, so I thought I would use it for the full run but the data from the run seems to be poor.

For background, i am running some short amplicons for detection of mammals from eDNA samples. I removed all of the non-biological sequences with Cutadapt prior to running DADA2. The amplicons are around 110 bp.

The quality plot looks like this,

Which is like nothing I have seen before. Why are there not Whisker plots at most positions?

For reference, this is what the plot looked like for the pilot MiSeq run:

Any thoughts would be helpful.

[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…