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 | 1700 | L1700L | L2518L | syn | ctC | ctT | 1277 | 1161 | 0.909162 | 7817-7819 |
ORF1ab/nsp3 | 1700 | L1700L | L2518L | syn | ctC | ctA | 1277 | 111 | 0.0869225 | 7817-7819 |
ORF1ab/nsp3 | 1700 | L1700L | L2518L | syn | ctC | ctG | 1277 | 4 | 0.00313234 | 7817-7819 |
ORF1ab/nsp3 | 1700 | L1700L | L2518L | syn | CtC | TtA | 1277 | 1 | 0.000783085 | 7817-7819 |
Details of the mutation L1700L 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 | 1700 | L1700L | ctC | ctT | 1161 | 1277 | All | 0.000222 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 111 | 1277 | All | 0.000021 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctG | 4 | 1277 | All | 0.000001 |
ORF1ab/nsp3 | 1700 | L1700L | CtC | TtA | 1 | 1277 | All | 0 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 341 | 366 | B.1.1.7 | 0.000305 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 25 | 366 | B.1.1.7 | 0.000022 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 54 | 76 | AY.4 | 0.000084 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 22 | 76 | AY.4 | 0.000034 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 73 | 74 | AY.3 | 0.000726 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 74 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 38 | 44 | B.1.617.2 | 0.000143 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 6 | 44 | B.1.617.2 | 0.000023 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 42 | 42 | P.1 | 0.000662 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 31 | 32 | AY.43 | 0.000137 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 32 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 30 | 30 | N.10 | 0.882353 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 29 | 29 | AY.47 | 0.000902 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 29 | 29 | B.1.526 | 0.000682 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 27 | 27 | AY.25 | 0.000162 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 23 | 27 | B.1 | 0.000211 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 4 | 27 | B.1 | 0.000037 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 26 | 26 | AY.26 | 0.000736 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 26 | 26 | B.1.1.50 | 0.017651 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 26 | 26 | B.1.2 | 0.000229 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 24 | 25 | AY.44 | 0.000146 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 25 | AY.44 | 0.000006 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 21 | 21 | B.1.427 | 0.00106 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 19 | 19 | AY.57 | 0.012467 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 10 | 18 | AY.103 | 0.000062 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 8 | 18 | AY.103 | 0.00005 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 14 | 18 | B.1.177 | 0.000184 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 4 | 18 | B.1.177 | 0.000053 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 18 | 18 | Q.1 | 0.002274 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 13 | 13 | B.1.1.284 | 0.001396 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 13 | 13 | B.1.1.413 | 0.089655 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 9 | 11 | B.1.1.33 | 0.003788 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 2 | 11 | B.1.1.33 | 0.000842 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 11 | 11 | B.1.538 | 0.08871 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 10 | 10 | B.1.177.21 | 0.000765 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 9 | 9 | B.1.369 | 0.002567 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 8 | 8 | AY.23 | 0.000558 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 8 | 8 | B.1.627 | 0.016162 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 7 | 7 | AY.9.2 | 0.000257 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 6 | 7 | B.1.351 | 0.000178 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 7 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 5 | 6 | AY.102 | 0.000133 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 6 | AY.102 | 0.000027 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 6 | 6 | AY.77 | 0.006764 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 6 | 6 | B.1.1.519 | 0.000238 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 5 | 5 | AY.14 | 0.00044 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 5 | 5 | B.1.1.214 | 0.000277 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 5 | B.1.258 | 0.0002 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctG | 2 | 5 | B.1.258 | 0.000133 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 5 | 5 | W.1 | 0.043478 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | AY.39 | 0.000099 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | AY.46.4 | 0.000658 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 3 | 4 | AY.61 | 0.000314 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 4 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | AY.99.2 | 0.000369 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | B.1.179 | 0.015038 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | B.1.265 | 0.005083 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | B.1.595 | 0.001044 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | B.1.621 | 0.000354 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | B.1.628 | 0.001409 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 4 | 4 | P.1.16 | 0.001496 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | AY.100 | 0.000138 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | AY.20 | 0.000117 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 2 | 3 | AY.46 | 0.000208 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 3 | AY.46 | 0.000104 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | AY.79 | 0.003632 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | B.1.1.113 | 0.020979 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | B.1.1.306 | 0.001315 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | B.1.177.52 | 0.005272 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | B.1.243 | 0.000209 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | B.1.482 | 0.25 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 3 | 3 | P.2 | 0.00056 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 3 | 3 | Q.4 | 0.001364 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1700 | L1700L | CtC | TtA | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | AY.16 | 0.000759 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctG | 1 | 2 | AY.3.1 | 0.000085 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 2 | AY.3.1 | 0.000085 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | AY.59 | 0.001059 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | AY.98 | 0.000158 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 2 | B.1.1.222 | 0.000204 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 2 | B.1.1.222 | 0.000204 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | B.1.1.28 | 0.000622 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | B.1.1.311 | 0.000716 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 2 | 2 | B.1.177.87 | 0.001456 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 2 | 2 | B.1.351.2 | 0.000605 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 2 | 2 | B.1.400 | 0.000858 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | B.1.575 | 0.000607 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | C.16 | 0.002121 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | C.26 | 0.014706 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | C.37 | 0.000232 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 2 | 2 | Q.8 | 0.00033 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 1 | AY.104 | 0.001984 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctG | 1 | 1 | AY.116.1 | 0.000311 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.50 | 0.000799 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.55 | 0.000917 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.69 | 0.000187 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.7.1 | 0.000113 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 1 | AY.7.2 | 0.000559 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.1.207 | 0.001182 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.1.322 | 0.008772 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.1.373 | 0.02381 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.1.434 | 0.000349 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.1.440 | 0.011765 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 1 | B.1.157 | 0.002985 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.36.8 | 0.001 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.36.9 | 0.003215 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.389 | 0.001002 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.438.1 | 0.000107 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctA | 1 | 1 | B.6.6 | 0.000889 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | C.32 | 0.023256 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | C.37.1 | 0.002618 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | P.1.2 | 0.001156 |
ORF1ab/nsp3 | 1700 | L1700L | ctC | ctT | 1 | 1 | P.1.7 | 0.000319 |
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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