Add nucleotide mutations to characteristic mutations

[flaneuse]

Suggested in #279; related to #265 and #258.

Would require changes to API and front-end.

[flaneuse]

Suggested again from a user to the help account: "While the amino acid mutations are super useful, a list of the defining nucleotide mutations for each variant is equally important, particularly for checking the impact of these mutations on diagnostic tests i.e. PCR primer/probe sequences."

[bwlang]

B.1.621 has a characteristic 4 nt deletion in the N gene del:26158:4 (see https://github.com/cov-lineages/pango-designation/issues/57) but this is not seen in the comparison view https://outbreak.info/compare-lineages?pango=B.1.621&pango=B.1.617.2&gene=ORF1a&gene=ORF1b&gene=S&gene=ORF8&gene=N&gene=ORF10&gene=ORF3a&gene=E&gene=M&gene=ORF7a&gene=ORF6&gene=ORF7b&threshold=75&dark=false might make that easier to show.

An option to show nt space might make that easier to show (also it doesn't quite render correctly with the copy button in my hands).

[gkarthik]

Hey @bwlang, I think the 4 nucleotide deletion you are referring to is in ORF3A. It is currently numbered DEL257/257 but we have a pull request (https://github.com/andersen-lab/bjorn/pull/28) to fix the numbering. Should be out soon.

I agree that showing the nucleotide numbers would be useful.

[bwlang]

ah! - you're right - that is ORF3a - thanks!

[EmilyHaag]

User suggested via survey: Add search by RNA mutation as well as by protein mutation

[EmilyHaag]

User suggested via email that they would like to '...access the nucleotide mutations corresponding to the characteristic amino acid mutation tables for alpha, beta, etc.'