I am currently using Qiime2 on 16S paired-end data for the V3-V4 region. Everything works smoothly up to the point I get the relative frequencies per group. I get 63% of a specific family (e.g.Enterobacteriaceae) while the rest are taxonomically assigned at the genus level. My question is if this is normal. Is it possible that the taxonomic analysis cannot go deeper (at genus level) for such a big amount of features? What would be your suggestions in that case?
Thanks a lot!