BUG: "Mutations on branch" in tree view list "reversions" in unsequenced parts of genome

[corneliusroemer]

When I upload a truncated sequence, that's missing half of S gene for example, the mutations on branch in tree view display "reversions" for parts of the sequence that were chopped off.

The highlighted parts should not be displayed there. It looks like the gene mutations are not aware of missing parts of the sequence if the sequence is truncated. See #730 for a possibly related manifestation.

I wonder where the root of the problem is. When we extract genes for translation, don't we pad unsequenced parts with Ns so they would show as Xs in the peptide?

[corneliusroemer]

Out of curiosity, I looked at how we output the aligned peptide in this case of truncation.

We seem to call the truncated parts as deletions. Is that on purpose? It would feel more appropriate to call them X I feel. It's much more likely that a partial gene was uploaded than that this is a real deletion.