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Usher SARS-CoV-2 masks quite a lot of sites (I think around 270, i.e. almost 1% of genome) based on this vcf: https://raw.githubusercontent.com/W-L/ProblematicSites_SARS-CoV2/master/problematic_sites_…
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I worked a bit on the labelling matching with ENA / NCBI as I had a lot of mismatch issues with the development of the FAIR Data Station. I forked the repo and did an analysis on the terms in MIxS and…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/2108
KP.3.1.1+G21893A(S:D111N)
S:D111N is one of the newly-emerged beneficial mutations on KP.3.1.1 backbone. 16% global advant…
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Related to #1762.
When you create the "Ensembl Transcript" and "Ensembl Peptide" sections on the protein pages of arabidopsis, fruitfly, yeast and sarscov2 e.g.
https://api.glygen.org/protein/d…
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There seem to be several people in the introductions thread (#17 ) who are interested in zoonotic diseases, a topic that is currently missing from [the introduction section outline](greenelab/covid19-…
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transferred from: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1653
tree: https://nextstr…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1888
KP.3.3.1+G15543T+C21998A(S:H146N)
GISAID query: C21998A, G15543T,C23202A
No. of seqs: 33(USA 2(1 from Turkey) Japan 3(1…
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There seems to be a very new and very interesting branch of XEC found by @FedeGueli 。
From branch 13 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/2088
XEC+G2060A(Orf1a:A599T)+C…
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From branch 18 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1771
sub branch of #2668
KP.2.3+del21653_21655(S:S31-)+C28714T+A6184C(Orf1a:R1973S)+A29647G+C21691T,G22132T,A22995…
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From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1919
KP.3.3+G18274T(Orf1b:A1603S)+del29581(Orf10 frameshift)+T21738C(S:F59S)
GISAID query: G18274T,T21738C,G28884C
No. of se…