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GenSpectrum / cov-spectrum-website

A web platform to detect and analyze variants of SARS-CoV-2
https://cov-spectrum.org
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BUG: mutation nuc:C11956T cannot be displayed correctly if one choose "Show amino acid and nucleotide mutations together" #737

Open AnonymousUserUse opened 1 year ago

AnonymousUserUse commented 1 year ago

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.

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@chaoran-chen

AnonymousUserUse commented 1 year ago

Push @chaoran-chen @corneliusroemer @Sinickle

chaoran-chen commented 1 year ago

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.

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

AnonymousUserUse commented 1 year ago

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.