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corneliusroemer / pango-sequences

Consensus sequences for each Pango lineage
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error in `aaSubstitutions` for JN.1 #8

Closed jbloom closed 5 months ago

jbloom commented 5 months ago

@corneliusroemer, I think you have some bug for your aaSubstitutions field for JN.1. My understanding is that this is supposed to have spike amino-acid mutations relative to the Wuhan-Hu-1 reference, but it only reports two spike mutations.

Things seem correct for both BA.2.86 and JN.1.1, so I think the problem is unique to JN.1.

I am looking at this file: https://raw.githubusercontent.com/corneliusroemer/pango-sequences/main/data/pango-consensus-sequences_summary.json

corneliusroemer commented 5 months ago

Thanks @jbloom for reporting! It is indeed a bug, due to a frameshift almost certainly because Nextclade doesn't output AA muts past a frameshift.

It's likely because there are only 2 JN.1 sequences designated (after most have been redesignated as sublineages).

I'll let you know once I've fixed it!

Yep, it's a frameshift, see the other fields:

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jbloom commented 5 months ago

Great, thanks. And as always, thanks so much for maintaining this list of clade founders. I use it so much which is why I stumble on things like this ;)

corneliusroemer commented 5 months ago

It's fixed now! Thanks for reporting again!

One thing that's sadly still missing is insertions