Hi @aghudson,
Thank you for the update!
It seems surprising that many ASVs are dropping. Are the per-sample read counts dropping much? I ask because in other scenarios, I've seen the number of ASVs drop a fair amount however the retained sequence data is still like > 99%, suggesting most lost were singletons.
The mapping for non-v4-16s is a known issue. The underlying plugin, q2-vsearch, does not emit the mapping information so that the moment we cannot readily expose that. We've recently opened an issue about it, and the seed of that discussion can be found here (Introducing Greengenes2 2022.10 - #34 by wasade).
Best,
Daniel