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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1738
A new Orf9b mutation occurs under KP.3.3. Note that Orf9b mutations are not shown on usher so hard to notice.
KP.3.3+A97…
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from @adamkucharski
``` r
# Get libraries
library(superspreading)
library(epiparameter)
# Load parameters
sars Using Lloyd-Smith J, Schreiber S, Kopp P, Getz W (2005). "Superspreading and
…
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Triples like this (this is for Rhea but I also want the same for Reactome reaction IDs):
```
.
```
![image](https://github.com/glygener/glygen-issues/assets/20584876/6d956be5-e1f8-44d1-b262…
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data organization
Directory to submit the data to Mac: smb://cfscloud.nist.gov/midas_uploads/2714
__ONT__
files on oneDrive under **SARs-CoV-2-RGTM**
- Raw fast5s
- Basecalled fastqs
- Seq…
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If an OpenShift user has `edit` permissions to the namespace, we should assign superuser permissions to the user in Netbox and remove them if they don't.
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Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1643
KP.2.2+C23277T(S:T572I)
GISAID query: C23277T, A25359G, T21737C, -A2745G, -24364,-28468,-25455,-29410
No. of …
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1806
KS.1.1--JN.1
Breakpoint between 22929 and 24820
Additional mutations: C6701T, C19716T, T25510C, C29311T
Orf1a:L214…
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From branch 9 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
JN.1.4+T18453C+del21653_21655,G22599C,A27675C(S:S31del, S:R346T, Orf7a:Q94H)
I cannot decide the order.
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From branch 4 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1768
KP.2+C5673T(Orf1a:P1803L)+C14220T+C3619T, C18657T,G23236T, C26936T, del21656_21658(S:K558N, F32del)
GISAID q…
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KP.1.1+C21774A,del21653_21655(S:S71Y, S31del)
This is another re-proposal due to inaccurate proposal by DailyCovidCases.
From branch 34 of https://github.com/sars-cov-2-variants/lineage-proposal…