Dropping in QC of FASTAQ

[s_farraj]

Hi all,
We have MiseqDX and we upgraded it to be compatible with 600cycles kit.
We made after that 2 runs:
The first one was for 16srRNA library following the recommended protocol from illumina (It doesn't depend on any library preparation kit). We used 600cycles kit.
The second run is for whole genome sequencing for different species (viruses & bacteria). We used Nextera XT kit with 300cycle kit.
In both runs when we check the QC for the fastaq files we found a systematic dropping in all samples. I mean by dropping, the quality score reduced to near 2 then returns back to 37 in all the samples in the run (the pictures attached for the QC for one of the samples in each run, the rest samples are the same).
The dropping in the first run was in R1 from cycle 5 to cycle 20.
In the second run, The dropping was in R2 from cycle 30 to 75 cycle.

Did anyone face problem like this?
Is there any explanation for this situation?

Thanks

[GenoMax]

You must have a region of low nucleotide diversity in that region in the middle (e.g. A's in majority of clusters at that cycle) which leads to these drops in qualities. Can you post nucleotide distribution plot from FastQC?

What version chemistry is this? What is cluster density and PF%? Was phiX spiked in and at what concentration?

[s_farraj]

Thanks for your quick response.
I attached the Fasta QC report for the sample for the second run and pic for its data.
This run didn't have Phix.
But like I said in the previous post, this was for whole genome sequences for different species.
This one was V2 but the first run was with V3.

[thermophile]

check your thumbnails. I'd guess that your density is actually much higher than 1300-genomes should have very high PF

[s_farraj]

Thanks for your answer
Today the engineering come and check these runs and he said its over clustered
I think I will reduce the conc. of pooling library from 10pM to 6pM hoping avoid this dropping issue.