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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1645
KP.2.3+C28714T+A1087G+A23166C(S:K535T)
GISAID query: C28714T,A1087G,A23166C
No. of seqs: 37(USA 3 France 1 Spain 1 UK 32)…
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### Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1573
**Description**
**Sub-lineage of:** KP.3.1 (JN.1.11.1.3 = JN.1 + S:F456L, Q493E, V1104L)
**Earliest sequenc…
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Hi there,
I created a PanGraph of 200 SARS-CoV-2 sequences using FASTA sequences as input, and it seems that eleven of them aren't represented incorrectly in the JSON file. I have uploaded the data…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1503
JN.1+T20285C,A20284T(Orf1b:I2273S)+G22599C,T22928C(S:R346T,F456L)
GISAID query:T20285C, A20284T, C18894T, G22599C,T22928…
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There is a growing need for people to assign their sequences to clades and do some simple QC. In the longer term, we also want to support running augur on SARS-CoV-2 data in the cloud. I imagine a col…
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Proteins use these tax IDs:
```
"tax_id","short_name","long_name","common_name","nt_file","is_reference","sort_order"
"9606","human","Homo sapiens","Human","uniprot-proteome-homo-sapiens.nt","yes",…
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From branch 64 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1+C22858T+S:F456L
Query: C22858T,T22928C,C18894T,-7113
No. of seqs: 23 (South Korea 21 Japan 1 USA 1)
Fir…
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From branch 74 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1.34+Orf1a:T2846R, S100R, E386D+S:F456L
Query: C23673T,T22928C, C8802T,T565A
No. of seqs: 23 (Denmark 1 Fra…
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From branch 49 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1 > S:H1101Y ( C24863T )>S:F456L (T22928C)
Query:C24863T, T22928C, T3565C
No. of seqs: 25 (Canada 1 China …
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From branch 30 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253
JN.1.26+S:F456L
Query: C26894T, C7732T,G22599C, T22928C
No. of seqs: 32 (Canada 26 USA 6)
First: EPI_ISL_1894…