I am analyzing phytoplankton samples from a lake. A lot of uncultured or unassigned Organisms showed up in my Taxonomy Barplot file. So I wanted to manually determine the taxa using BLASTn. I chose to exclude Uncultured/environmental sample sequences and used "Highly similar sequences (megablast)".
Here is a screenshot of my results.
I moved your post to the “other bioinformatics tools” category, as it is fundamentally about interpreting NCBI BLAST results, so not a “user support” type question (for QIIME 2).
That said, it does touch on a user support issue with QIIME 2:
This is very often a technical issue, e.g., incorrect use of the classifier or problems with the reference database. See here for some troubleshooting steps:
This is usually one of the first things I do for diagnosing this issue, too. Since you are getting lots of hits to Telonema I think it is worth asking: is this in your reference database? You can follow the troubleshooting steps I linked to above to determine if this is an issue relating to the query or reference sequences, or some other issue. Any time NCBI BLAST finds a good hit (as you have), q2-feature-classifier should in theory be able to as well and there is a user error keeping it from doing so.
They all have the same query coverage, but a couple stand out as having much higher percent identity… and hence higher scores and lower E values than the others.