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 | 1429 | T1429T | T2247T | syn | acC | acT | 2597 | 2501 | 0.963034 | 7004-7006 |
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 | 1429 | T1429T | acC | acT | 2501 | 2597 | All | 0.000478 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 426 | 426 | B.1.36.38 | 0.699507 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 257 | 274 | B.1.1.7 | 0.00023 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 229 | 229 | AY.14 | 0.020155 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 130 | 130 | B.1.429 | 0.003059 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 125 | 129 | AY.4 | 0.000195 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 120 | 120 | B.1.349 | 0.085776 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 87 | 93 | AY.44 | 0.00053 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 82 | 85 | B.1 | 0.000751 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 80 | 80 | AB.1 | 0.655738 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 71 | 77 | B.1.617.2 | 0.000267 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 60 | 68 | B.1.2 | 0.000528 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 51 | 51 | P.1 | 0.000803 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 47 | 47 | AY.103 | 0.000292 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 40 | 45 | AY.43 | 0.000177 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 41 | 41 | B.1.1.394 | 1 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 28 | 28 | B.1.177.18 | 0.032483 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 20 | 21 | B.1.525 | 0.002263 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 19 | 19 | AY.25 | 0.000114 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 8 | 18 | AY.3 | 0.00008 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 17 | 17 | B.1.36.33 | 0.128788 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 16 | 16 | AY.5 | 0.00033 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 16 | 16 | AY.64 | 0.009524 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 11 | 16 | B.1.221 | 0.000781 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 14 | 15 | B.1.1 | 0.000254 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 14 | 14 | AY.6 | 0.000576 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 14 | 14 | B.1.160 | 0.000437 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 14 | 14 | B.1.36 | 0.002043 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 13 | 13 | AY.4.2 | 0.000282 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 13 | 13 | B.1.258 | 0.000865 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 13 | 13 | B.1.258.17 | 0.001352 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 12 | 12 | AY.29 | 0.000189 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 12 | 12 | B.1.177 | 0.000158 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 12 | 12 | B.1.351 | 0.000357 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 11 | 11 | AY.26 | 0.000311 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 10 | 10 | B.1.234 | 0.001319 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 9 | 10 | B.1.617.1 | 0.001161 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 10 | 10 | B.1.628 | 0.003524 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 9 | 9 | AY.100 | 0.000414 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 8 | 9 | AY.119 | 0.000282 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 9 | 9 | B.1.1.306 | 0.003946 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 8 | 8 | AY.118 | 0.000501 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 7 | 8 | AY.39 | 0.000173 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 8 | 8 | AY.46 | 0.000833 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 8 | 8 | B.1.625 | 0.018824 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 7 | 7 | AY.102 | 0.000186 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 7 | 7 | AY.42 | 0.000282 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 6 | 6 | AY.113 | 0.000854 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 6 | 6 | AY.19 | 0.006842 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 6 | 6 | AY.27 | 0.000388 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 6 | 6 | AY.85 | 0.002563 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 6 | 6 | B.1.1.519 | 0.000238 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 6 | 6 | B.1.177.42 | 0.005367 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 6 | 6 | B.1.367 | 0.004754 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 5 | 5 | AY.116 | 0.001434 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 5 | AY.20 | 0.000155 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 5 | 5 | AY.39.1 | 0.000198 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 5 | 5 | AY.9.1 | 0.000419 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 5 | 5 | B.1.1.309 | 0.02924 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 5 | 5 | B.1.160.14 | 0.010593 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 5 | 5 | P.1.15 | 0.001162 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 5 | 5 | P.1.2 | 0.00578 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 4 | AD.2 | 0.000219 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | AY.32 | 0.00213 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | AY.34 | 0.000388 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 4 | AY.47 | 0.000093 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | AY.49 | 0.01278 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | AY.5.3 | 0.00135 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 4 | AY.5.4 | 0.00083 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | AY.98.1 | 0.000194 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | B.1.1.311 | 0.001433 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | B.1.1.317 | 0.001647 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | B.1.177.44 | 0.002076 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 4 | 4 | B.1.243 | 0.000278 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 4 | P.1.14 | 0.000143 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | AY.37 | 0.000948 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | AY.45 | 0.000365 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | AY.54 | 0.000286 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 3 | AY.61 | 0.00021 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | AY.93 | 0.000819 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | AY.98 | 0.000237 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | AY.99.2 | 0.000276 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | AZ.1 | 0.002602 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.1.157 | 0.00274 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.1.231 | 0.009288 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.1.253 | 0.007519 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.1.301 | 0.003538 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.1.318 | 0.000905 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.1.500 | 0.06 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.1.89 | 0.018182 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.177.86 | 0.00055 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 3 | 3 | B.1.427 | 0.000151 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 3 | B.1.637 | 0.000073 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | A.21 | 0.00554 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | AY.114 | 0.000462 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | AY.95 | 0.001522 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.1.161 | 0.007067 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.1.214 | 0.000111 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.1.216 | 0.001781 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.1.398 | 0.006452 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.1.448 | 0.004065 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.1.71 | 0.012121 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.111 | 0.00235 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.177.21 | 0.000153 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.177.34 | 0.105263 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.177.43 | 0.002954 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.177.68 | 0.030303 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.206 | 0.001631 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | B.1.396 | 0.001411 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 2 | 2 | Q.1 | 0.000253 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | 0.055556 | |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AK.1 | 0.012658 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.120.2 | 0.001285 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.41 | 0.000294 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.56 | 0.001605 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.79 | 0.001211 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.86 | 0.00083 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | AY.96 | 0.002075 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.184 | 0.058824 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.27 | 0.00565 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.277 | 0.000759 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.37 | 0.000193 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.482 | 0.023256 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.487 | 0.005587 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.63 | 0.000386 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.1.95 | 0.019608 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.110.3 | 0.000718 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.126 | 0.001276 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.160.9 | 0.007194 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.177.35 | 0.000691 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.232 | 0.000537 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.351.3 | 0.000876 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.36.22 | 0.001208 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.509 | 0.000866 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.540 | 0.009709 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.575 | 0.000303 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.598 | 0.016949 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.600 | 0.005848 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.618 | 0.004032 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.619 | 0.000871 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.1.619.1 | 0.000641 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.20 | 0.023256 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | B.61 | 0.005747 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | C.36.2 | 0.034483 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | P.1.17 | 0.000162 |
ORF1ab/nsp3 | 1429 | T1429T | acC | acT | 1 | 1 | R.1 | 0.00009 |
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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