Hi @liang_zhou,
Thank you for the detail on the commands run!
When using non-v4-16s, the plugin executes the q2-vsearch closed reference OTU picking pipeline against the backbone sequences. The features expressed in the resulting table will be a subset of the backbone. The exact code applied is here.
With 16S V4 ASVs, if using filter-features, the resulting features will be a subset of the V4 ASVs that have previously been placed into Greengenes2.
I'm not aware of a means to do that through QIIME 2 right now. The q2-vsearch's cluster_features_closed_reference action does not appear to return the UC mapping that describes the query / subject relationship. That mapping is necessary to determine what ASVs recruit to which backbone records.
@gregcaporaso I don't think there is a mechanism right now with q2-vsearch to obtain the mapping detail. Would that be valuable? If so I'll open an issue to track it
Best,
Daniel