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 |
N | 292 | I292T | nonsyn | aTc | aCc | 4675 | 4520 | 0.966845 | 29147-29149 | |
N | 292 | I292T | nonsyn | aTC | aCT | 4675 | 155 | 0.0331551 | 29147-29149 |
Details of the mutation I292T 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 |
N | 292 | I292T | aTc | aCc | 4520 | 4675 | All | 0.000865 |
N | 292 | I292T | aTC | aCT | 155 | 4675 | All | 0.00003 |
N | 292 | I292T | aTc | aCc | 2353 | 2363 | B.1.1.33 | 0.99032 |
N | 292 | I292T | aTC | aCT | 10 | 2363 | B.1.1.33 | 0.004209 |
N | 292 | I292T | aTc | aCc | 395 | 538 | N.5 | 0.69788 |
N | 292 | I292T | aTC | aCT | 143 | 538 | N.5 | 0.25265 |
N | 292 | I292T | aTc | aCc | 234 | 235 | N.4 | 0.995745 |
N | 292 | I292T | aTC | aCT | 1 | 235 | N.4 | 0.004255 |
N | 292 | I292T | aTc | aCc | 229 | 229 | B.1.1 | 0.004154 |
N | 292 | I292T | aTc | aCc | 172 | 172 | N.3 | 1 |
N | 292 | I292T | aTc | aCc | 164 | 164 | N.9 | 0.97619 |
N | 292 | I292T | aTc | aCc | 140 | 140 | N.6 | 0.992908 |
N | 292 | I292T | aTc | aCc | 127 | 127 | B.1.1.7 | 0.000114 |
N | 292 | I292T | aTc | aCc | 96 | 96 | B.1.160.16 | 0.089219 |
N | 292 | I292T | aTc | aCc | 83 | 84 | B.1 | 0.00076 |
N | 292 | I292T | aTC | aCT | 1 | 84 | B.1 | 0.000009 |
N | 292 | I292T | aTc | aCc | 42 | 42 | N.1 | 0.711864 |
N | 292 | I292T | aTc | aCc | 34 | 34 | N.10 | 1 |
N | 292 | I292T | aTc | aCc | 34 | 34 | N.7 | 1 |
N | 292 | I292T | aTc | aCc | 32 | 32 | N.8 | 1 |
N | 292 | I292T | aTc | aCc | 31 | 31 | AY.25 | 0.000186 |
N | 292 | I292T | aTc | aCc | 26 | 26 | AK.1 | 0.329114 |
N | 292 | I292T | aTc | aCc | 26 | 26 | AY.4 | 0.00004 |
N | 292 | I292T | aTc | aCc | 26 | 26 | N.2 | 1 |
N | 292 | I292T | aTc | aCc | 19 | 19 | B.1.139 | 0.01393 |
N | 292 | I292T | aTc | aCc | 19 | 19 | B.1.177.44 | 0.00986 |
N | 292 | I292T | aTc | aCc | 18 | 18 | AY.44 | 0.00011 |
N | 292 | I292T | aTc | aCc | 17 | 17 | B.1.1.519 | 0.000675 |
N | 292 | I292T | aTc | aCc | 10 | 10 | B.1.2 | 0.000088 |
N | 292 | I292T | aTc | aCc | 10 | 10 | B.1.617.2 | 0.000038 |
N | 292 | I292T | aTc | aCc | 9 | 9 | AY.3 | 0.00009 |
N | 292 | I292T | aTc | aCc | 9 | 9 | B.1.160 | 0.000281 |
N | 292 | I292T | aTc | aCc | 9 | 9 | B.1.351 | 0.000268 |
N | 292 | I292T | aTc | aCc | 8 | 8 | B.1.177.75 | 0.008325 |
N | 292 | I292T | aTc | aCc | 8 | 8 | B.1.429 | 0.000188 |
N | 292 | I292T | aTc | aCc | 7 | 7 | AY.102 | 0.000186 |
N | 292 | I292T | aTc | aCc | 7 | 7 | B.1.1.393 | 0.777778 |
N | 292 | I292T | aTc | aCc | 7 | 7 | B.1.177 | 0.000092 |
N | 292 | I292T | aTc | aCc | 7 | 7 | B.1.609 | 0.003356 |
N | 292 | I292T | aTc | aCc | 7 | 7 | P.1 | 0.00011 |
N | 292 | I292T | aTc | aCc | 6 | 6 | AY.43 | 0.000027 |
N | 292 | I292T | aTc | aCc | 6 | 6 | AZ.5 | 0.021053 |
N | 292 | I292T | aTc | aCc | 6 | 6 | B.1.1.28 | 0.001867 |
N | 292 | I292T | aTc | aCc | 5 | 5 | AY.34 | 0.000485 |
N | 292 | I292T | aTc | aCc | 4 | 4 | AY.75 | 0.000224 |
N | 292 | I292T | aTc | aCc | 4 | 4 | B.1.221 | 0.000284 |
N | 292 | I292T | aTc | aCc | 3 | 3 | AY.20 | 0.000117 |
N | 292 | I292T | aTc | aCc | 3 | 3 | AY.42 | 0.000121 |
N | 292 | I292T | aTc | aCc | 3 | 3 | B.1.1.303 | 0.008287 |
N | 292 | I292T | aTc | aCc | 2 | 2 | 0.111111 | |
N | 292 | I292T | aTc | aCc | 2 | 2 | AY.119 | 0.000071 |
N | 292 | I292T | aTc | aCc | 2 | 2 | AY.29 | 0.000032 |
N | 292 | I292T | aTc | aCc | 2 | 2 | AY.39 | 0.000049 |
N | 292 | I292T | aTc | aCc | 2 | 2 | AY.46.2 | 0.001271 |
N | 292 | I292T | aTc | aCc | 2 | 2 | AY.47 | 0.000062 |
N | 292 | I292T | aTc | aCc | 2 | 2 | B.1.1.318 | 0.000604 |
N | 292 | I292T | aTc | aCc | 2 | 2 | B.1.36.18 | 0.00084 |
N | 292 | I292T | aTc | aCc | 2 | 2 | B.1.499 | 0.002101 |
N | 292 | I292T | aTc | aCc | 2 | 2 | B.1.526 | 0.000047 |
N | 292 | I292T | aTc | aCc | 2 | 2 | B.1.596 | 0.000174 |
N | 292 | I292T | aTc | aCc | 2 | 2 | B.4 | 0.004415 |
N | 292 | I292T | aTc | aCc | 1 | 1 | A.2 | 0.000662 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.103 | 0.000006 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.117 | 0.000085 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.13 | 0.000161 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.2 | 0.000356 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.23 | 0.00007 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.26 | 0.000028 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.39.1 | 0.00004 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.46.1 | 0.001027 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.68 | 0.000274 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.73 | 0.000665 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.79 | 0.001211 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.9.2 | 0.000037 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.93 | 0.000273 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.98.1 | 0.000048 |
N | 292 | I292T | aTc | aCc | 1 | 1 | AY.99.2 | 0.000092 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.1.27 | 0.00565 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.1.332 | 0.03125 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.1.356 | 0.008547 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.1.362 | 0.005618 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.1.70 | 0.000341 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.104 | 0.00369 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.170 | 0.00431 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.177.51 | 0.004566 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.177.73 | 0.000566 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.201 | 0.005682 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.258 | 0.000067 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.404 | 0.001302 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.459 | 0.004082 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.466.2 | 0.000391 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.479 | 0.038462 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.621 | 0.000089 |
N | 292 | I292T | aTc | aCc | 1 | 1 | B.1.91 | 0.002075 |
N | 292 | I292T | aTc | aCc | 1 | 1 | C.1.2 | 0.004255 |
N | 292 | I292T | aTc | aCc | 1 | 1 | C.27 | 0.018519 |
N | 292 | I292T | aTc | aCc | 1 | 1 | C.37 | 0.000116 |
N | 292 | I292T | aTc | aCc | 1 | 1 | C.39 | 0.018868 |
N | 292 | I292T | aTc | aCc | 1 | 1 | P.1.12 | 0.000484 |
N | 292 | I292T | aTc | aCc | 1 | 1 | P.1.15 | 0.000232 |
N | 292 | I292T | aTc | aCc | 1 | 1 | P.1.7 | 0.000319 |
N | 292 | I292T | aTc | aCc | 1 | 1 | P.2 | 0.000187 |
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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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