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 |
S | 859 | T859N | nonsyn | aCt | aAt | 24827 | 24818 | 0.999637 | 24137-24139 | |
S | 859 | T859N | nonsyn | aCT | aAC | 24827 | 9 | 0.000362509 | 24137-24139 |
Details of the mutation T859N 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 |
S | 859 | T859N | aCt | aAt | 24818 | 24827 | All | 0.004747 |
S | 859 | T859N | aCT | aAC | 9 | 24827 | All | 0.000002 |
S | 859 | T859N | aCt | aAt | 13341 | 13348 | B.1.637 | 0.974863 |
S | 859 | T859N | aCT | aAC | 7 | 13348 | B.1.637 | 0.000512 |
S | 859 | T859N | aCt | aAt | 8533 | 8535 | C.37 | 0.990367 |
S | 859 | T859N | aCT | aAC | 2 | 8535 | C.37 | 0.000232 |
S | 859 | T859N | aCt | aAt | 548 | 548 | B.1 | 0.005019 |
S | 859 | T859N | aCt | aAt | 368 | 368 | C.37.1 | 0.963351 |
S | 859 | T859N | aCt | aAt | 307 | 307 | B.1.36.9 | 0.987138 |
S | 859 | T859N | aCt | aAt | 251 | 251 | B.1.617.2 | 0.000945 |
S | 859 | T859N | aCt | aAt | 212 | 212 | C.1.2 | 0.902128 |
S | 859 | T859N | aCt | aAt | 173 | 173 | B.1.626 | 0.988571 |
S | 859 | T859N | aCt | aAt | 140 | 140 | B.1.1 | 0.00254 |
S | 859 | T859N | aCt | aAt | 127 | 127 | B.1.415.1 | 0.962121 |
S | 859 | T859N | aCt | aAt | 65 | 65 | AY.102 | 0.001723 |
S | 859 | T859N | aCt | aAt | 49 | 49 | AY.46.6 | 0.003538 |
S | 859 | T859N | aCt | aAt | 44 | 44 | B.1.639 | 0.956522 |
S | 859 | T859N | aCt | aAt | 41 | 41 | B.1.1.524 | 0.854167 |
S | 859 | T859N | aCt | aAt | 38 | 38 | AY.43 | 0.000168 |
S | 859 | T859N | aCt | aAt | 36 | 36 | C.40 | 1 |
S | 859 | T859N | aCt | aAt | 32 | 32 | C.36.3.1 | 0.086957 |
S | 859 | T859N | aCt | aAt | 28 | 28 | B.1.214.2 | 0.016787 |
S | 859 | T859N | aCt | aAt | 27 | 27 | AY.92 | 0.007756 |
S | 859 | T859N | aCt | aAt | 26 | 26 | B.1.526 | 0.000611 |
S | 859 | T859N | aCt | aAt | 22 | 22 | B.1.2 | 0.000194 |
S | 859 | T859N | aCt | aAt | 21 | 21 | B.1.576 | 0.019039 |
S | 859 | T859N | aCt | aAt | 19 | 19 | AY.39 | 0.00047 |
S | 859 | T859N | aCt | aAt | 17 | 17 | B.1.633 | 0.708333 |
S | 859 | T859N | aCt | aAt | 16 | 16 | B.1.1.7 | 0.000014 |
S | 859 | T859N | aCt | aAt | 14 | 14 | P.1.15 | 0.003253 |
S | 859 | T859N | aCt | aAt | 12 | 12 | B | 0.001534 |
S | 859 | T859N | aCt | aAt | 12 | 12 | B.1.638 | 0.631579 |
S | 859 | T859N | aCt | aAt | 11 | 11 | AY.36 | 0.00163 |
S | 859 | T859N | aCt | aAt | 11 | 11 | B.1.1.372 | 0.007576 |
S | 859 | T859N | aCt | aAt | 10 | 10 | P.1 | 0.000158 |
S | 859 | T859N | aCt | aAt | 9 | 9 | AY.103 | 0.000056 |
S | 859 | T859N | aCt | aAt | 8 | 8 | AY.44 | 0.000049 |
S | 859 | T859N | aCt | aAt | 7 | 7 | AY.25 | 0.000042 |
S | 859 | T859N | aCt | aAt | 7 | 7 | B.1.1.1 | 0.002287 |
S | 859 | T859N | aCt | aAt | 7 | 7 | B.1.1.28 | 0.002179 |
S | 859 | T859N | aCt | aAt | 7 | 7 | B.1.177.73 | 0.003964 |
S | 859 | T859N | aCt | aAt | 7 | 7 | B.1.632 | 0.04698 |
S | 859 | T859N | aCt | aAt | 7 | 7 | B.1.636 | 0.04698 |
S | 859 | T859N | aCt | aAt | 6 | 6 | B.1.177.7 | 0.000989 |
S | 859 | T859N | aCt | aAt | 6 | 6 | B.1.596 | 0.000523 |
S | 859 | T859N | aCt | aAt | 6 | 6 | B.1.623 | 0.003219 |
S | 859 | T859N | aCt | aAt | 5 | 5 | AY.84 | 0.002187 |
S | 859 | T859N | aCt | aAt | 5 | 5 | B.1.36 | 0.00073 |
S | 859 | T859N | aCt | aAt | 5 | 5 | P.1.12 | 0.00242 |
S | 859 | T859N | aCt | aAt | 5 | 5 | P.5 | 0.068493 |
S | 859 | T859N | aCt | aAt | 4 | 4 | AY.23 | 0.000279 |
S | 859 | T859N | aCt | aAt | 4 | 4 | AY.3 | 0.00004 |
S | 859 | T859N | aCt | aAt | 4 | 4 | AY.4 | 0.000006 |
S | 859 | T859N | aCt | aAt | 4 | 4 | AY.42 | 0.000161 |
S | 859 | T859N | aCt | aAt | 4 | 4 | AY.9.2 | 0.000147 |
S | 859 | T859N | aCt | aAt | 4 | 4 | AY.98 | 0.000316 |
S | 859 | T859N | aCt | aAt | 4 | 4 | B.1.427 | 0.000202 |
S | 859 | T859N | aCt | aAt | 4 | 4 | B.1.618 | 0.016129 |
S | 859 | T859N | aCt | aAt | 4 | 4 | P.1.1 | 0.001271 |
S | 859 | T859N | aCt | aAt | 3 | 3 | AY.13 | 0.000483 |
S | 859 | T859N | aCt | aAt | 3 | 3 | AY.26 | 0.000085 |
S | 859 | T859N | aCt | aAt | 3 | 3 | AY.45 | 0.000365 |
S | 859 | T859N | aCt | aAt | 3 | 3 | AY.46 | 0.000312 |
S | 859 | T859N | aCt | aAt | 3 | 3 | AY.5 | 0.000062 |
S | 859 | T859N | aCt | aAt | 3 | 3 | B.1.1.412 | 0.022901 |
S | 859 | T859N | aCt | aAt | 3 | 3 | B.1.1.507 | 0.026087 |
S | 859 | T859N | aCt | aAt | 3 | 3 | B.1.1.528 | 0.014423 |
S | 859 | T859N | aCt | aAt | 3 | 3 | B.1.351 | 0.000089 |
S | 859 | T859N | aCt | aAt | 3 | 3 | B.1.609 | 0.001438 |
S | 859 | T859N | aCt | aAt | 3 | 3 | C.39 | 0.056604 |
S | 859 | T859N | aCt | aAt | 3 | 3 | P.1.17 | 0.000485 |
S | 859 | T859N | aCt | aAt | 3 | 3 | Q.8 | 0.000495 |
S | 859 | T859N | aCt | aAt | 2 | 2 | AY.108 | 0.002205 |
S | 859 | T859N | aCt | aAt | 2 | 2 | AY.5.3 | 0.000675 |
S | 859 | T859N | aCt | aAt | 2 | 2 | AY.52 | 0.001629 |
S | 859 | T859N | aCt | aAt | 2 | 2 | AY.61 | 0.00021 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.1.265 | 0.006309 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.1.291 | 0.001485 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.1.294 | 0.002532 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.1.318 | 0.000604 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.1.519 | 0.000079 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.160 | 0.000062 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.177 | 0.000026 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.311 | 0.000549 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.336 | 0.004878 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.36.31 | 0.003503 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.36.8 | 0.002 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.404 | 0.002604 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.413 | 0.008511 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.621 | 0.000177 |
S | 859 | T859N | aCt | aAt | 2 | 2 | B.1.9.5 | 0.011364 |
S | 859 | T859N | aCt | aAt | 2 | 2 | C.1 | 0.004785 |
S | 859 | T859N | aCt | aAt | 1 | 1 | A.2 | 0.000662 |
S | 859 | T859N | aCt | aAt | 1 | 1 | A.2.5 | 0.000499 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.100 | 0.000046 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.107 | 0.000466 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.119 | 0.000035 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.120 | 0.000037 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.15 | 0.002222 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.3.1 | 0.000085 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.30 | 0.000396 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.35 | 0.000233 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.39.1 | 0.00004 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.4.2 | 0.000022 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.55 | 0.000917 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.58 | 0.000907 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.60 | 0.000938 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.99 | 0.001049 |
S | 859 | T859N | aCt | aAt | 1 | 1 | AY.99.2 | 0.000092 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.1.220 | 0.001859 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.1.222 | 0.000204 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.1.348 | 0.000796 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.1.409 | 0.002833 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.1.413 | 0.006897 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.1.448 | 0.002033 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.177.44 | 0.000519 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.177.79 | 0.002342 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.177.81 | 0.000189 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.208 | 0.04 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.214 | 0.003663 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.221 | 0.000071 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.241 | 0.000812 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.243.1 | 0.022222 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.258 | 0.000067 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.280 | 0.007143 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.324 | 0.001605 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.338 | 0.008621 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.350 | 0.002933 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.356 | 0.001727 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.36.10 | 0.004785 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.367 | 0.000792 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.375 | 0.00082 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.399 | 0.001934 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.411 | 0.003704 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.429 | 0.000024 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.451 | 0.008197 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.462 | 0.007246 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.533 | 0.009615 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.575 | 0.000303 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.582 | 0.000491 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.617.1 | 0.000129 |
S | 859 | T859N | aCt | aAt | 1 | 1 | B.1.628 | 0.000352 |
S | 859 | T859N | aCt | aAt | 1 | 1 | C.14 | 0.004329 |
S | 859 | T859N | aCt | aAt | 1 | 1 | C.35 | 0.000774 |
S | 859 | T859N | aCt | aAt | 1 | 1 | C.4 | 0.01 |
S | 859 | T859N | aCt | aAt | 1 | 1 | P.1.16 | 0.000374 |
S | 859 | T859N | aCt | aAt | 1 | 1 | Q.4 | 0.000455 |
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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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