BUG: mutation nuc:C11956T cannot be displayed correctly if one choose "Show amino acid and nucleotide mutations together"

[AnonymousUserUse]

I do not know the exact problem behind this, so I just report the bug that I met:
When I e.g. search for the variant XBB.1.9* (https://cov-spectrum.org/explore/World/AllSamples/Past2M/variants?nextcladePangoLineage=XBB.1.9*&), which partly contains the mutation nuc:C11956T, I can see this mutation in the list of nucleotide mutations.
However, if I choose "Show amino acid and nucleotide mutations together", the mutation nuc:C11956T disappeared.

@chaoran-chen

[AnonymousUserUse]

Push @chaoran-chen @corneliusroemer @Sinickle

[chaoran-chen]

Hi @AnonymousUserUse, thank you very much for reporting this, and sorry for the very late reply! The reason for it is that the 11956 position corresponds to ORF1a:3897 where we have the mutation ORF1a:D3897G with a very low prevalence of 0.04%. This is causing it not to appear by default but only if we change the proportion filter.

That's not very intuitive and we will try to make it better.

[AnonymousUserUse]

Thanks for the explanation. @chaoran-chen
It seems that this problem occurs very frequently in large lineages.
I hope that nucleotide mutations corresponding to amino acid mutations that have a prevalence outside the selected range can also be shown in "additional nucleotide mutations" in the future.
Maybe this issue can be added to the to-do-list.