CoV-GLUE | Mutations | Mutation
Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):
ORF | CodonNum | Mut | ORF1abMut | MutType | RefCodon | MutCodon | AACount | CodonCount | CodonProp | Genome Position |
ORF1ab/nsp3 | 1288 | T1288del | T2106del | del | ACT | --- | 309 | 309 | 1 | 6581-6583 |
Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):
ORF | CodonNum | Mut | RefCodon | MutCodon | CodonCount | AACount | Lineage | LineageCodonProp |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 309 | 309 | All | 0.000059 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 127 | 127 | B.1.1.7 | 0.000114 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 40 | 40 | AY.26 | 0.001132 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 19 | 19 | B.1.177 | 0.00025 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 15 | 15 | AY.4 | 0.000023 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 8 | 8 | AY.4.5 | 0.00086 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 7 | 7 | AY.43 | 0.000031 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 7 | 7 | B.1.617.2 | 0.000026 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 4 | 4 | B.1.1 | 0.000073 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 3 | 3 | B.1.1.1 | 0.00098 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 3 | 3 | B.1.177.7 | 0.000495 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 3 | 3 | B.1.36.17 | 0.001482 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | AY.19 | 0.002281 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | AY.5 | 0.000041 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | AY.75.1 | 0.000361 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | AY.9 | 0.000135 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | B.1.1.37 | 0.000386 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 2 | 2 | B.1.177.4 | 0.000422 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AD.2 | 0.000219 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.59 | 0.00053 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.60 | 0.000938 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.221 | 0.010101 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.258 | 0.003257 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.312 | 0.001912 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.348 | 0.000796 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.361 | 0.045455 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.44 | 0.00241 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.11 | 0.001698 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.15 | 0.000631 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.16 | 0.000664 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.17 | 0.000821 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.52 | 0.001757 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.56 | 0.000668 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.177.9 | 0.001332 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.221.1 | 0.002907 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.258.10 | 0.011364 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.279 | 0.000514 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.340 | 0.004292 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.36.39 | 0.002217 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.389 | 0.001002 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.409 | 0.000781 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.585 | 0.027778 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.588 | 0.00091 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.617.3 | 0.002985 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.1.630 | 0.005236 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | B.34 | 0.013699 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp3 | 1288 | T1288del | ACT | --- | 1 | 1 | U.3 | 0.003861 |
CoV-GLUE is still in development. CoV-GLUE was originally developed as part of COG-UK by Josh Singer using the GLUE framework at the MRC-University of Glasgow Centre for Virus Research (CVR). In 2021 it was redeveloped by Richard Orton to scale to the millions of genome sequences available. We acknowledge support from the MRC (MC_UU_12014/12), WT (220977/Z/20/Z) and UKRI G2P (MR/W005611/1). Please contact Richard Orton with any queries: Richard.Orton@glasgow.ac.uk
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