![I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but low quality q30 <40%. Kindly advice what could get wrong? I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but low quality q30 <40%. Kindly advice what could get wrong?](https://www.researchgate.net/profile/Amit-Chaurasia-4/post/I-had-a-Metagenomic-16s-rRNA-run-on-MiSeq-v3-kit-2-x300-cycles-with-good-PF-89-but-low-quality-q30-40-Kindly-advice-what-could-get-wrong/attachment/5ad1b986b53d2f63c3c5bdc4/AS%3A615231206223873%401523693958893/download/1.png)
I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but low quality q30 <40%. Kindly advice what could get wrong?
![The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces. - Abstract - Europe PMC The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces. - Abstract - Europe PMC](https://europepmc.org/articles/PMC5914283/bin/sdata201868-f1.jpg)
The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces. - Abstract - Europe PMC
![An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform | Microbiome | Full Text An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform | Microbiome | Full Text](https://media.springernature.com/lw685/springer-static/image/art%3A10.1186%2F2049-2618-2-6/MediaObjects/40168_2013_Article_35_Fig1_HTML.jpg)
An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform | Microbiome | Full Text
![I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but low quality q30 <40%. Kindly advice what could get wrong? I had a Metagenomic 16s rRNA run on MiSeq v3 kit 2 x300 cycles. with good PF >89% but low quality q30 <40%. Kindly advice what could get wrong?](https://www.researchgate.net/profile/Amit-Chaurasia-4/post/I-had-a-Metagenomic-16s-rRNA-run-on-MiSeq-v3-kit-2-x300-cycles-with-good-PF-89-but-low-quality-q30-40-Kindly-advice-what-could-get-wrong/attachment/5ad1b987b53d2f63c3c5bdc5/AS%3A615231206215687%401523693958972/download/2.png)