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Big thanks to @Over-There-Is
From: https://github.com/sars-cov-2-variants/lineage-proposals/issues/2023
![image](https://github.com/user-attachments/assets/798ae78f-c081-44fa-90d4-097f18d43924)
tr…
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Are only recombination events that have the QC flag of PASS worth reporting or investigating closer, and all others to be excluded?
I was wondering if pango-designation recombinants like XBC and XB…
fgmp updated
2 months ago
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This issue contains two examples of visualising recombinants.
For this issue I've chosen to display BA.1, BA.2, BA.4 and BA.5 as distinct recombinants, however that choice is clearly up for grabs. …
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1. region CP022323.1:983,532-1,047,672 in DA163 has a CNV
2. This sample also has a good deal of long inserts
3. After repeat masking, are either the CNV or the long inserts affect?
4. With long in…
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KP.2.3--KP.3.2.3
breakpoint between 22600 and 22857
Additional mutations: G974A, G2323A, C12710T, C14688T, C19118T,del21653_21655, C28695T
Orf1a: E237K
Orf1b:A1884V
Orf3a:W69C
S:S31-
N:T141…
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Successor issue of https://github.com/sars-cov-2-variants/lineage-proposals/issues/991
> Anything with >5 reversion(refer to the last checkpoint ,usually a designation) or >20 private mutations(di…
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### Current Behavior
Augur export converts literals to lower case in its stderr output - which is probably not what we want
### Expected behavior
Literals are output as they are, not changing cas…
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There seems to be an LF.1.1.1 branch that loses Orf1a mutations due to recombinant.
JN.1--LF.1.1.1
Breakpoint between 6574 and 16550
It is basically LF.1.1.1 losing G4067A and C6573T. It keep…
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This week (2022-04-17), I noticed the [public trees](http://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/) have a new(?) nomenclature for recombinant lineages that takes the format `mis…
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Hi there,
First, thanks for your work and the latest updates!
We stumbled across a few samples from the last months that pangolin assigns to a top-level lineage, namely BA.2 or XBB.1.
The nextc…