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 |
M | 150 | R150R | syn | cgT | cgC | 25715 | 25704 | 0.999572 | 26970-26972 | |
M | 150 | R150R | syn | cgT | cgG | 25715 | 10 | 0.000388878 | 26970-26972 | |
M | 150 | R150R | syn | cgT | cgA | 25715 | 1 | 0.0000388878 | 26970-26972 | |
M | 150 | R150del | del | CGT | --- | 125 | 125 | 1 | 26970-26972 | |
M | 150 | R150C | nonsyn | Cgt | Tgt | 11 | 8 | 0.727273 | 26970-26972 | |
M | 150 | R150C | nonsyn | CgT | TgC | 11 | 3 | 0.272727 | 26970-26972 | |
M | 150 | R150L | nonsyn | cGt | cTt | 10 | 10 | 1 | 26970-26972 | |
M | 150 | R150S | nonsyn | Cgt | Agt | 6 | 4 | 0.666667 | 26970-26972 | |
M | 150 | R150S | nonsyn | CgT | AgC | 6 | 2 | 0.333333 | 26970-26972 | |
M | 150 | R150del1 | del | Cgt | -gt | 3 | 1 | 0.333333 | 26970-26972 | |
M | 150 | R150del1 | del | cGt | c-t | 3 | 1 | 0.333333 | 26970-26972 | |
M | 150 | R150del1 | del | cgT | cg- | 3 | 1 | 0.333333 | 26970-26972 | |
M | 150 | R150P | nonsyn | cGt | cCt | 2 | 2 | 1 | 26970-26972 | |
M | 150 | R150H | nonsyn | cGt | cAt | 2 | 2 | 1 | 26970-26972 | |
M | 150 | R150del2 | del | CGt | --t | 2 | 1 | 0.5 | 26970-26972 | |
M | 150 | R150del2 | del | CGT | --G | 2 | 1 | 0.5 | 26970-26972 | |
M | 150 | R150Q | nonsyn | cGT | cAG | 1 | 1 | 1 | 26970-26972 |
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 |
M | 150 | R150R | cgT | cgC | 25704 | 25715 | All | 0.004916 |
M | 150 | R150R | cgT | cgG | 10 | 25715 | All | 0.000002 |
M | 150 | R150R | cgT | cgA | 1 | 25715 | All | 0 |
M | 150 | R150R | cgT | cgC | 10324 | 10324 | B.1.258 | 0.68703 |
M | 150 | R150R | cgT | cgC | 9413 | 9413 | B.1.258.17 | 0.978686 |
M | 150 | R150R | cgT | cgC | 2483 | 2483 | B.1.258.11 | 0.984146 |
M | 150 | R150R | cgT | cgC | 523 | 523 | B.1.258.7 | 1 |
M | 150 | R150R | cgT | cgC | 372 | 372 | B.1.258.22 | 0.992 |
M | 150 | R150R | cgT | cgC | 290 | 290 | B.1.258.4 | 1 |
M | 150 | R150R | cgT | cgC | 255 | 255 | B.1 | 0.002336 |
M | 150 | R150R | cgT | cgC | 198 | 198 | B.1.258.9 | 0.99 |
M | 150 | R150R | cgT | cgC | 141 | 141 | B.1.1.7 | 0.000126 |
M | 150 | R150R | cgT | cgC | 141 | 141 | B.1.258.19 | 1 |
M | 150 | R150del | CGT | --- | 125 | 125 | All | 0.000024 |
M | 150 | R150R | cgT | cgC | 125 | 125 | B.1.258.12 | 0.984252 |
M | 150 | R150R | cgT | cgC | 125 | 125 | B.1.258.21 | 0.968992 |
M | 150 | R150R | cgT | cgC | 114 | 114 | B.1.258.5 | 1 |
M | 150 | R150R | cgT | cgC | 113 | 113 | B.1.617.2 | 0.000425 |
M | 150 | R150del | CGT | --- | 102 | 102 | B.1.177.21 | 0.0078 |
M | 150 | R150R | cgT | cgC | 95 | 99 | AY.4 | 0.000148 |
M | 150 | R150R | cgT | cgG | 4 | 99 | AY.4 | 0.000006 |
M | 150 | R150R | cgT | cgC | 87 | 87 | B.1.258.10 | 0.988636 |
M | 150 | R150R | cgT | cgC | 63 | 63 | B.1.258.20 | 1 |
M | 150 | R150R | cgT | cgC | 57 | 61 | AY.3 | 0.000567 |
M | 150 | R150R | cgT | cgG | 4 | 61 | AY.3 | 0.00004 |
M | 150 | R150R | cgT | cgC | 53 | 53 | AY.44 | 0.000323 |
M | 150 | R150R | cgT | cgC | 51 | 51 | B.1.258.6 | 1 |
M | 150 | R150R | cgT | cgC | 44 | 44 | B.1.621 | 0.003895 |
M | 150 | R150R | cgT | cgC | 41 | 41 | B.1.258.23 | 0.97619 |
M | 150 | R150R | cgT | cgC | 37 | 37 | B.1.2 | 0.000326 |
M | 150 | R150R | cgT | cgC | 35 | 35 | B.1.177 | 0.000461 |
M | 150 | R150R | cgT | cgC | 35 | 35 | B.1.221 | 0.002486 |
M | 150 | R150R | cgT | cgC | 31 | 31 | B.1.258.24 | 0.333333 |
M | 150 | R150R | cgT | cgC | 30 | 30 | B.1.1 | 0.000544 |
M | 150 | R150R | cgT | cgC | 30 | 30 | B.1.160 | 0.000936 |
M | 150 | R150R | cgT | cgC | 29 | 29 | AY.103 | 0.00018 |
M | 150 | R150R | cgT | cgC | 28 | 28 | B.1.609 | 0.013423 |
M | 150 | R150R | cgT | cgC | 26 | 26 | AY.36 | 0.003854 |
M | 150 | R150R | cgT | cgC | 14 | 14 | B.1.367 | 0.011094 |
M | 150 | R150R | cgT | cgC | 13 | 13 | B | 0.001662 |
M | 150 | R150del | CGT | --- | 13 | 13 | B.1.1.7 | 0.000012 |
M | 150 | R150R | cgT | cgC | 13 | 13 | B.1.258.14 | 0.012745 |
M | 150 | R150R | cgT | cgC | 13 | 13 | B.1.418 | 0.206349 |
M | 150 | R150R | cgT | cgC | 12 | 12 | AY.25 | 0.000072 |
M | 150 | R150R | cgT | cgC | 12 | 12 | AY.39 | 0.000297 |
M | 150 | R150R | cgT | cgC | 12 | 12 | AY.43 | 0.000053 |
M | 150 | R150C | Cgt | Tgt | 8 | 11 | All | 0.000002 |
M | 150 | R150C | CgT | TgC | 3 | 11 | All | 0.000001 |
M | 150 | R150L | cGt | cTt | 10 | 10 | All | 0.000002 |
M | 150 | R150R | cgT | cgC | 10 | 10 | B.1.258.18 | 1 |
M | 150 | R150R | cgT | cgC | 9 | 9 | B.1.234 | 0.001187 |
M | 150 | R150R | cgT | cgC | 8 | 8 | A | 0.003096 |
M | 150 | R150R | cgT | cgC | 8 | 8 | AY.7.1 | 0.000902 |
M | 150 | R150R | cgT | cgC | 7 | 7 | AY.4.2 | 0.000152 |
M | 150 | R150R | cgT | cgC | 7 | 7 | B.1.1.519 | 0.000278 |
M | 150 | R150R | cgT | cgC | 7 | 7 | B.1.222 | 0.011844 |
M | 150 | R150R | cgT | cgC | 7 | 7 | B.4.1 | 0.132075 |
M | 150 | R150S | Cgt | Agt | 4 | 6 | All | 0.000001 |
M | 150 | R150S | CgT | AgC | 2 | 6 | All | 0 |
M | 150 | R150R | cgT | cgC | 6 | 6 | AY.100 | 0.000276 |
M | 150 | R150R | cgT | cgC | 6 | 6 | AY.91 | 0.004383 |
M | 150 | R150R | cgT | cgC | 6 | 6 | B.1.375 | 0.004918 |
M | 150 | R150R | cgT | cgC | 5 | 5 | A.3 | 0.010482 |
M | 150 | R150R | cgT | cgC | 5 | 5 | AY.47 | 0.000156 |
M | 150 | R150R | cgT | cgC | 5 | 5 | B.1.411 | 0.018519 |
M | 150 | R150R | cgT | cgC | 5 | 5 | B.1.600 | 0.02924 |
M | 150 | R150R | cgT | cgC | 5 | 5 | P.1 | 0.000079 |
M | 150 | R150R | cgT | cgC | 4 | 4 | AY.46.6 | 0.000289 |
M | 150 | R150R | cgT | cgC | 4 | 4 | B.1.525 | 0.000453 |
M | 150 | R150R | cgT | cgC | 4 | 4 | R.1 | 0.00036 |
M | 150 | R150del1 | Cgt | -gt | 1 | 3 | All | 0 |
M | 150 | R150del1 | cgT | cg- | 1 | 3 | All | 0 |
M | 150 | R150del1 | cGt | c-t | 1 | 3 | All | 0 |
M | 150 | R150R | cgT | cgC | 3 | 3 | AY.77 | 0.003382 |
M | 150 | R150R | cgT | cgC | 3 | 3 | AY.98.1 | 0.000145 |
M | 150 | R150L | cGt | cTt | 3 | 3 | B.1 | 0.000027 |
M | 150 | R150R | cgT | cgC | 3 | 3 | B.1.160.8 | 0.003866 |
M | 150 | R150C | CgT | TgC | 3 | 3 | B.1.177.21 | 0.000229 |
M | 150 | R150R | cgT | cgC | 2 | 3 | B.1.177.73 | 0.001133 |
M | 150 | R150R | cgT | cgA | 1 | 3 | B.1.177.73 | 0.000566 |
M | 150 | R150R | cgT | cgC | 3 | 3 | B.1.258.15 | 0.056604 |
M | 150 | R150R | cgT | cgC | 3 | 3 | B.1.429 | 0.000071 |
M | 150 | R150R | cgT | cgC | 3 | 3 | Q.3 | 0.000435 |
M | 150 | R150H | cGt | cAt | 2 | 2 | All | 0 |
M | 150 | R150P | cGt | cCt | 2 | 2 | All | 0 |
M | 150 | R150del2 | CGT | --G | 1 | 2 | All | 0 |
M | 150 | R150del2 | CGt | --t | 1 | 2 | All | 0 |
M | 150 | R150R | cgT | cgC | 2 | 2 | AY.102 | 0.000053 |
M | 150 | R150R | cgT | cgC | 2 | 2 | AY.119 | 0.000071 |
M | 150 | R150R | cgT | cgC | 2 | 2 | AY.3.1 | 0.000171 |
M | 150 | R150R | cgT | cgC | 2 | 2 | AY.40 | 0.001929 |
M | 150 | R150R | cgT | cgC | 2 | 2 | AY.59 | 0.001059 |
M | 150 | R150R | cgT | cgC | 2 | 2 | AY.75.1 | 0.000361 |
M | 150 | R150C | Cgt | Tgt | 2 | 2 | B.1 | 0.000018 |
M | 150 | R150S | Cgt | Agt | 1 | 2 | B.1 | 0.000009 |
M | 150 | R150S | CgT | AgC | 1 | 2 | B.1 | 0.000009 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.1.153 | 0.002191 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.1.214 | 0.000111 |
M | 150 | R150L | cGt | cTt | 2 | 2 | B.1.1.7 | 0.000002 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.1.70 | 0.000682 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.160.7 | 0.004158 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.177.31 | 0.022989 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.177.6 | 0.001953 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.177.7 | 0.00033 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.237 | 0.00995 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.351 | 0.000059 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.36 | 0.000292 |
M | 150 | R150R | cgT | cgG | 2 | 2 | B.1.36.1 | 0.002281 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.466.2 | 0.000782 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.576 | 0.001813 |
M | 150 | R150R | cgT | cgC | 2 | 2 | B.1.590 | 0.009091 |
M | 150 | R150R | cgT | cgC | 1 | 1 | 0.055556 | |
M | 150 | R150R | cgT | cgC | 1 | 1 | A.2.4 | 0.003367 |
M | 150 | R150R | cgT | cgC | 1 | 1 | A.2.5 | 0.000499 |
M | 150 | R150Q | cGT | cAG | 1 | 1 | All | 0 |
M | 150 | R150del2 | CGT | --G | 1 | 1 | AY.103 | 0.000006 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.11 | 0.001339 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.16.1 | 0.00047 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.20 | 0.000039 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.23 | 0.00007 |
M | 150 | R150del2 | CGt | --t | 1 | 1 | AY.25 | 0.000006 |
M | 150 | R150del | CGT | --- | 1 | 1 | AY.26 | 0.000028 |
M | 150 | R150L | cGt | cTt | 1 | 1 | AY.27 | 0.000065 |
M | 150 | R150L | cGt | cTt | 1 | 1 | AY.4 | 0.000002 |
M | 150 | R150S | CgT | AgC | 1 | 1 | AY.42 | 0.00004 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.42 | 0.00004 |
M | 150 | R150del | CGT | --- | 1 | 1 | AY.43 | 0.000004 |
M | 150 | R150del | CGT | --- | 1 | 1 | AY.44 | 0.000006 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.45 | 0.000122 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.46.4 | 0.000165 |
M | 150 | R150P | cGt | cCt | 1 | 1 | AY.47 | 0.000031 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.52 | 0.000814 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.61 | 0.000105 |
M | 150 | R150C | Cgt | Tgt | 1 | 1 | AY.61 | 0.000105 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.62 | 0.000436 |
M | 150 | R150S | Cgt | Agt | 1 | 1 | AY.7.1 | 0.000113 |
M | 150 | R150Q | cGT | cAG | 1 | 1 | AY.85 | 0.000427 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.9 | 0.000068 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.98 | 0.000079 |
M | 150 | R150R | cgT | cgC | 1 | 1 | AY.99.2 | 0.000092 |
M | 150 | R150H | cGt | cAt | 1 | 1 | B.1 | 0.000009 |
M | 150 | R150del | CGT | --- | 1 | 1 | B.1 | 0.000009 |
M | 150 | R150H | cGt | cAt | 1 | 1 | B.1.1 | 0.000018 |
M | 150 | R150C | Cgt | Tgt | 1 | 1 | B.1.1 | 0.000018 |
M | 150 | R150del | CGT | --- | 1 | 1 | B.1.1.221 | 0.010101 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.1.225 | 0.007194 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.1.284 | 0.000107 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.1.317 | 0.000412 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.1.39 | 0.00051 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.1.409 | 0.002833 |
M | 150 | R150del | CGT | --- | 1 | 1 | B.1.1.420 | 0.001006 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.1.466 | 0.008696 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.1.50 | 0.000679 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.146 | 0.004237 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.149 | 0.003425 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.157 | 0.002985 |
M | 150 | R150L | cGt | cTt | 1 | 1 | B.1.177 | 0.000013 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.177.12 | 0.000152 |
M | 150 | R150del1 | Cgt | -gt | 1 | 1 | B.1.177.35 | 0.000691 |
M | 150 | R150C | Cgt | Tgt | 1 | 1 | B.1.177.52 | 0.001757 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.177.80 | 0.001912 |
M | 150 | R150C | Cgt | Tgt | 1 | 1 | B.1.177.86 | 0.000183 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.177.86 | 0.000183 |
M | 150 | R150S | Cgt | Agt | 1 | 1 | B.1.2 | 0.000009 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.223 | 0.002778 |
M | 150 | R150L | cGt | cTt | 1 | 1 | B.1.232 | 0.000537 |
M | 150 | R150C | Cgt | Tgt | 1 | 1 | B.1.234 | 0.000132 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.242 | 0.018868 |
M | 150 | R150del | CGT | --- | 1 | 1 | B.1.258.11 | 0.000396 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.258.16 | 0.001637 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.258.3 | 0.001675 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.293 | 0.0125 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.329 | 0.000608 |
M | 150 | R150del | CGT | --- | 1 | 1 | B.1.351 | 0.00003 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.36.17 | 0.000494 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.36.31 | 0.001751 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.36.9 | 0.003215 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.362 | 0.001541 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.366 | 0.004878 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.406 | 0.006061 |
M | 150 | R150del | CGT | --- | 1 | 1 | B.1.427 | 0.00005 |
M | 150 | R150P | cGt | cCt | 1 | 1 | B.1.429 | 0.000024 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.432 | 0.011236 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.524 | 0.001406 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.526 | 0.000024 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.596 | 0.000087 |
M | 150 | R150del1 | cgT | cg- | 1 | 1 | B.1.596 | 0.000087 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.599 | 0.00365 |
M | 150 | R150del | CGT | --- | 1 | 1 | B.1.617.2 | 0.000004 |
M | 150 | R150del1 | cGt | c-t | 1 | 1 | B.1.617.2 | 0.000004 |
M | 150 | R150L | cGt | cTt | 1 | 1 | B.1.617.2 | 0.000004 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.623 | 0.000536 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.627 | 0.00202 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.637 | 0.000073 |
M | 150 | R150R | cgT | cgC | 1 | 1 | B.1.94 | 0.027027 |
M | 150 | R150C | Cgt | Tgt | 1 | 1 | Q.1 | 0.000126 |
M | 150 | R150S | Cgt | Agt | 1 | 1 | Q.1 | 0.000126 |
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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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