Are you using
--p-trim-left to deal with the poor-quality positions at the 5’ end? Ideally, you keep those positions so that it’s easier to do meta-analysis, but if they’re causing a significant amount of sequence loss, it might be best to drop them.
The worst positions in your plots are clearly early in the early and late positions, but these “middle” positions might be relevant. For example, position 206 also drops to Q=26.
Try trimming off the bad positions at the beginning, and truncating at 205, and let’s see what happens.
Looking forward, please consider sharing
qzv files rather than
csvs. It often makes troubleshooting easier, because QIIME 2 artifacts include all the details of what commands you ran to produce them.