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 | 196 | Y196Y | syn | taC | taT | 1567 | 1567 | 1 | 27108-27110 | |
M | 196 | Y196del | del | TAC | --- | 178 | 178 | 1 | 27108-27110 | |
M | 196 | Y196H | nonsyn | Tac | Cac | 15 | 15 | 1 | 27108-27110 | |
M | 196 | Y196F | nonsyn | tAc | tTc | 12 | 11 | 0.916667 | 27108-27110 | |
M | 196 | Y196F | nonsyn | tAC | tTT | 12 | 1 | 0.0833333 | 27108-27110 | |
M | 196 | Y196X | nonsyn | taC | taA | 8 | 6 | 0.75 | 27108-27110 | |
M | 196 | Y196X | nonsyn | taC | taG | 8 | 2 | 0.25 | 27108-27110 | |
M | 196 | Y196C | nonsyn | tAc | tGc | 4 | 4 | 1 | 27108-27110 | |
M | 196 | Y196del1 | del | taC | ta- | 2 | 2 | 1 | 27108-27110 | |
M | 196 | Y196S | nonsyn | tAc | tCc | 2 | 2 | 1 | 27108-27110 | |
M | 196 | Y196V | nonsyn | TAC | GTT | 2 | 1 | 0.5 | 27108-27110 | |
M | 196 | Y196V | nonsyn | TAc | GTc | 2 | 1 | 0.5 | 27108-27110 | |
M | 196 | Y196D | nonsyn | TaC | GaT | 2 | 1 | 0.5 | 27108-27110 | |
M | 196 | Y196D | nonsyn | Tac | Gac | 2 | 1 | 0.5 | 27108-27110 | |
M | 196 | Y196T | nonsyn | TAC | ACA | 1 | 1 | 1 | 27108-27110 | |
M | 196 | Y196del2 | del | TAc | --c | 1 | 1 | 1 | 27108-27110 | |
M | 196 | Y196K | nonsyn | TaC | AaA | 1 | 1 | 1 | 27108-27110 |
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 | 196 | Y196Y | taC | taT | 1567 | 1567 | All | 0.0003 |
M | 196 | Y196Y | taC | taT | 323 | 323 | B.1.1.7 | 0.000289 |
M | 196 | Y196Y | taC | taT | 226 | 226 | B.1.1.46 | 0.9869 |
M | 196 | Y196del | TAC | --- | 178 | 178 | All | 0.000034 |
M | 196 | Y196del | TAC | --- | 147 | 147 | B.1.177.21 | 0.011241 |
M | 196 | Y196Y | taC | taT | 100 | 100 | B.1.617.2 | 0.000377 |
M | 196 | Y196Y | taC | taT | 74 | 74 | AY.4 | 0.000115 |
M | 196 | Y196Y | taC | taT | 57 | 57 | AY.44 | 0.000347 |
M | 196 | Y196Y | taC | taT | 52 | 52 | B.1 | 0.000476 |
M | 196 | Y196Y | taC | taT | 51 | 51 | P.1 | 0.000803 |
M | 196 | Y196Y | taC | taT | 50 | 50 | AY.3 | 0.000497 |
M | 196 | Y196Y | taC | taT | 47 | 47 | AY.25 | 0.000283 |
M | 196 | Y196Y | taC | taT | 42 | 42 | AY.43 | 0.000186 |
M | 196 | Y196Y | taC | taT | 35 | 35 | AY.75 | 0.001961 |
M | 196 | Y196Y | taC | taT | 34 | 34 | AY.103 | 0.000211 |
M | 196 | Y196Y | taC | taT | 29 | 29 | AY.120 | 0.001078 |
M | 196 | Y196Y | taC | taT | 29 | 29 | Q.1 | 0.003663 |
M | 196 | Y196Y | taC | taT | 25 | 25 | B.1.2 | 0.00022 |
M | 196 | Y196del | TAC | --- | 20 | 20 | B.1.1.7 | 0.000018 |
M | 196 | Y196Y | taC | taT | 19 | 19 | AY.47 | 0.000591 |
M | 196 | Y196Y | taC | taT | 17 | 17 | B.1.560 | 0.078704 |
M | 196 | Y196Y | taC | taT | 16 | 16 | AY.5 | 0.00033 |
M | 196 | Y196H | Tac | Cac | 15 | 15 | All | 0.000003 |
M | 196 | Y196Y | taC | taT | 15 | 15 | AY.26 | 0.000425 |
M | 196 | Y196Y | taC | taT | 14 | 14 | B.1.429 | 0.000329 |
M | 196 | Y196Y | taC | taT | 13 | 13 | B.1.526 | 0.000306 |
M | 196 | Y196Y | taC | taT | 13 | 13 | P.1.7 | 0.004151 |
M | 196 | Y196F | tAc | tTc | 11 | 12 | All | 0.000002 |
M | 196 | Y196F | tAC | tTT | 1 | 12 | All | 0 |
M | 196 | Y196Y | taC | taT | 12 | 12 | B.1.1 | 0.000218 |
M | 196 | Y196Y | taC | taT | 10 | 10 | B.1.243 | 0.000696 |
M | 196 | Y196Y | taC | taT | 9 | 9 | AY.39 | 0.000222 |
M | 196 | Y196Y | taC | taT | 9 | 9 | B.1.427 | 0.000454 |
M | 196 | Y196X | taC | taA | 6 | 8 | All | 0.000001 |
M | 196 | Y196X | taC | taG | 2 | 8 | All | 0 |
M | 196 | Y196Y | taC | taT | 8 | 8 | AY.33 | 0.000534 |
M | 196 | Y196Y | taC | taT | 8 | 8 | AY.9.1 | 0.00067 |
M | 196 | Y196Y | taC | taT | 7 | 7 | B.1.1.70 | 0.002387 |
M | 196 | Y196Y | taC | taT | 7 | 7 | B.1.588 | 0.006369 |
M | 196 | Y196Y | taC | taT | 6 | 6 | AY.102 | 0.000159 |
M | 196 | Y196Y | taC | taT | 6 | 6 | AY.61 | 0.000629 |
M | 196 | Y196Y | taC | taT | 6 | 6 | AY.98 | 0.000474 |
M | 196 | Y196Y | taC | taT | 6 | 6 | B.1.1.291 | 0.004454 |
M | 196 | Y196Y | taC | taT | 6 | 6 | B.1.426 | 0.006054 |
M | 196 | Y196Y | taC | taT | 6 | 6 | B.1.497 | 0.001889 |
M | 196 | Y196Y | taC | taT | 6 | 6 | C.37.1 | 0.015707 |
M | 196 | Y196Y | taC | taT | 5 | 5 | AY.100 | 0.00023 |
M | 196 | Y196Y | taC | taT | 5 | 5 | AY.20 | 0.000194 |
M | 196 | Y196Y | taC | taT | 5 | 5 | B.1.1.519 | 0.000199 |
M | 196 | Y196C | tAc | tGc | 4 | 4 | All | 0.000001 |
M | 196 | Y196Y | taC | taT | 4 | 4 | AY.9 | 0.00027 |
M | 196 | Y196Y | taC | taT | 4 | 4 | AY.9.2 | 0.000147 |
M | 196 | Y196H | Tac | Cac | 4 | 4 | B.1 | 0.000037 |
M | 196 | Y196del | TAC | --- | 4 | 4 | B.1 | 0.000037 |
M | 196 | Y196Y | taC | taT | 4 | 4 | B.1.1.434 | 0.001394 |
M | 196 | Y196Y | taC | taT | 4 | 4 | B.1.160 | 0.000125 |
M | 196 | Y196Y | taC | taT | 4 | 4 | B.1.177 | 0.000053 |
M | 196 | Y196Y | taC | taT | 4 | 4 | B.1.177.62 | 0.004768 |
M | 196 | Y196Y | taC | taT | 4 | 4 | B.1.36.8 | 0.004 |
M | 196 | Y196Y | taC | taT | 4 | 4 | D.2 | 0.0003 |
M | 196 | Y196F | tAc | tTc | 2 | 3 | 0.111111 | |
M | 196 | Y196F | tAC | tTT | 1 | 3 | 0.055556 | |
M | 196 | Y196Y | taC | taT | 3 | 3 | AY.34 | 0.000291 |
M | 196 | Y196Y | taC | taT | 3 | 3 | AY.36 | 0.000445 |
M | 196 | Y196Y | taC | taT | 3 | 3 | AY.4.2 | 0.000065 |
M | 196 | Y196X | taC | taA | 2 | 3 | B.1 | 0.000018 |
M | 196 | Y196X | taC | taG | 1 | 3 | B.1 | 0.000009 |
M | 196 | Y196Y | taC | taT | 3 | 3 | B.1.1.170 | 0.003741 |
M | 196 | Y196Y | taC | taT | 3 | 3 | B.1.1.222 | 0.000612 |
M | 196 | Y196Y | taC | taT | 3 | 3 | B.1.177.72 | 0.010169 |
M | 196 | Y196Y | taC | taT | 3 | 3 | B.1.177.77 | 0.002179 |
M | 196 | Y196Y | taC | taT | 3 | 3 | B.1.36 | 0.000438 |
M | 196 | Y196Y | taC | taT | 3 | 3 | B.1.617.1 | 0.000387 |
M | 196 | Y196Y | taC | taT | 3 | 3 | B.1.637 | 0.000219 |
M | 196 | Y196Y | taC | taT | 3 | 3 | R.1 | 0.00027 |
M | 196 | Y196D | TaC | GaT | 1 | 2 | 0.055556 | |
M | 196 | Y196D | Tac | Gac | 1 | 2 | 0.055556 | |
M | 196 | Y196V | TAc | GTc | 1 | 2 | 0.055556 | |
M | 196 | Y196V | TAC | GTT | 1 | 2 | 0.055556 | |
M | 196 | Y196S | tAc | tCc | 2 | 2 | All | 0 |
M | 196 | Y196del1 | taC | ta- | 2 | 2 | All | 0 |
M | 196 | Y196D | Tac | Gac | 1 | 2 | All | 0 |
M | 196 | Y196V | TAC | GTT | 1 | 2 | All | 0 |
M | 196 | Y196V | TAc | GTc | 1 | 2 | All | 0 |
M | 196 | Y196D | TaC | GaT | 1 | 2 | All | 0 |
M | 196 | Y196H | Tac | Cac | 2 | 2 | AY.103 | 0.000012 |
M | 196 | Y196Y | taC | taT | 2 | 2 | AY.119 | 0.000071 |
M | 196 | Y196Y | taC | taT | 2 | 2 | AY.23 | 0.000139 |
M | 196 | Y196Y | taC | taT | 2 | 2 | AY.65 | 0.001066 |
M | 196 | Y196Y | taC | taT | 2 | 2 | AY.71 | 0.00095 |
M | 196 | Y196del | TAC | --- | 2 | 2 | AY.75 | 0.000112 |
M | 196 | Y196Y | taC | taT | 2 | 2 | AY.75.1 | 0.000361 |
M | 196 | Y196Y | taC | taT | 2 | 2 | AY.98.1 | 0.000097 |
M | 196 | Y196Y | taC | taT | 2 | 2 | B.1.1.37 | 0.000386 |
M | 196 | Y196H | Tac | Cac | 2 | 2 | B.1.1.7 | 0.000002 |
M | 196 | Y196Y | taC | taT | 2 | 2 | B.1.128 | 0.001271 |
M | 196 | Y196Y | taC | taT | 2 | 2 | B.1.240 | 0.000431 |
M | 196 | Y196Y | taC | taT | 2 | 2 | B.1.351 | 0.000059 |
M | 196 | Y196Y | taC | taT | 2 | 2 | B.1.561 | 0.000794 |
M | 196 | Y196del1 | taC | ta- | 2 | 2 | B.1.627 | 0.00404 |
M | 196 | Y196F | tAc | tTc | 2 | 2 | B.3.1 | 0.003317 |
M | 196 | Y196Y | taC | taT | 2 | 2 | P.1.14 | 0.000096 |
M | 196 | Y196Y | taC | taT | 1 | 1 | 0.055556 | |
M | 196 | Y196del | TAC | --- | 1 | 1 | A | 0.000387 |
M | 196 | Y196Y | taC | taT | 1 | 1 | A.2.2 | 0.001689 |
M | 196 | Y196Y | taC | taT | 1 | 1 | A.2.4 | 0.003367 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AD.2 | 0.000219 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AE.3 | 0.032258 |
M | 196 | Y196del2 | TAc | --c | 1 | 1 | All | 0 |
M | 196 | Y196K | TaC | AaA | 1 | 1 | All | 0 |
M | 196 | Y196T | TAC | ACA | 1 | 1 | All | 0 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.101 | 0.00049 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.113 | 0.000142 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.118 | 0.000063 |
M | 196 | Y196del | TAC | --- | 1 | 1 | AY.118 | 0.000063 |
M | 196 | Y196T | TAC | ACA | 1 | 1 | AY.119 | 0.000035 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.12 | 0.000316 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.14 | 0.000088 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.16 | 0.00038 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.16.1 | 0.00047 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.23.1 | 0.000417 |
M | 196 | Y196H | Tac | Cac | 1 | 1 | AY.25 | 0.000006 |
M | 196 | Y196F | tAc | tTc | 1 | 1 | AY.25 | 0.000006 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.27 | 0.000065 |
M | 196 | Y196C | tAc | tGc | 1 | 1 | AY.3 | 0.00001 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.3.1 | 0.000085 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.32 | 0.000532 |
M | 196 | Y196X | taC | taA | 1 | 1 | AY.39 | 0.000025 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.39.1 | 0.00004 |
M | 196 | Y196S | tAc | tCc | 1 | 1 | AY.4 | 0.000002 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.4.2.1 | 0.000149 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.4.5 | 0.000107 |
M | 196 | Y196del2 | TAc | --c | 1 | 1 | AY.42 | 0.00004 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.42 | 0.00004 |
M | 196 | Y196del | TAC | --- | 1 | 1 | AY.43 | 0.000004 |
M | 196 | Y196H | Tac | Cac | 1 | 1 | AY.44 | 0.000006 |
M | 196 | Y196C | tAc | tGc | 1 | 1 | AY.44 | 0.000006 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.5.4 | 0.000277 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.67 | 0.000464 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.68 | 0.000274 |
M | 196 | Y196S | tAc | tCc | 1 | 1 | AY.71 | 0.000475 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.85 | 0.000427 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.92 | 0.000287 |
M | 196 | Y196Y | taC | taT | 1 | 1 | AY.99.1 | 0.001553 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B | 0.000128 |
M | 196 | Y196H | Tac | Cac | 1 | 1 | B | 0.000128 |
M | 196 | Y196F | tAc | tTc | 1 | 1 | B.1 | 0.000009 |
M | 196 | Y196C | tAc | tGc | 1 | 1 | B.1 | 0.000009 |
M | 196 | Y196F | tAc | tTc | 1 | 1 | B.1.1 | 0.000018 |
M | 196 | Y196X | taC | taA | 1 | 1 | B.1.1 | 0.000018 |
M | 196 | Y196K | TaC | AaA | 1 | 1 | B.1.1 | 0.000018 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.1.220 | 0.001859 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.1.256 | 0.013699 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.1.258 | 0.003257 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.1.317 | 0.000412 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.1.369 | 0.000446 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.1.413 | 0.006897 |
M | 196 | Y196del | TAC | --- | 1 | 1 | B.1.1.420 | 0.001006 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.1.526 | 0.003546 |
M | 196 | Y196F | tAc | tTc | 1 | 1 | B.1.1.7 | 0.000001 |
M | 196 | Y196X | taC | taA | 1 | 1 | B.1.1.70 | 0.000341 |
M | 196 | Y196F | tAc | tTc | 1 | 1 | B.1.104 | 0.00369 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.111 | 0.001175 |
M | 196 | Y196H | Tac | Cac | 1 | 1 | B.1.139 | 0.000733 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.160.23 | 0.004831 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.160.30 | 0.002976 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.177.56 | 0.000668 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.177.57 | 0.000281 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.177.75 | 0.001041 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.177.87 | 0.000728 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.189 | 0.004292 |
M | 196 | Y196H | Tac | Cac | 1 | 1 | B.1.2 | 0.000009 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.23 | 0.006061 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.234 | 0.000132 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.236 | 0.002053 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.258 | 0.000067 |
M | 196 | Y196del | TAC | --- | 1 | 1 | B.1.258.11 | 0.000396 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.258.17 | 0.000104 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.258.7 | 0.001912 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.289 | 0.00266 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.298 | 0.002114 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.351.3 | 0.000876 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.36.1 | 0.00114 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.36.10 | 0.004785 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.36.20 | 0.016949 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.399 | 0.001934 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.416 | 0.001269 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.428.2 | 0.033333 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.438.1 | 0.000107 |
M | 196 | Y196C | tAc | tGc | 1 | 1 | B.1.525 | 0.000113 |
M | 196 | Y196F | tAc | tTc | 1 | 1 | B.1.561 | 0.000397 |
M | 196 | Y196H | Tac | Cac | 1 | 1 | B.1.564 | 0.000426 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.565 | 0.00081 |
M | 196 | Y196X | taC | taA | 1 | 1 | B.1.567 | 0.003333 |
M | 196 | Y196X | taC | taG | 1 | 1 | B.1.617.2 | 0.000004 |
M | 196 | Y196F | tAc | tTc | 1 | 1 | B.1.617.2 | 0.000004 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.1.627 | 0.00202 |
M | 196 | Y196Y | taC | taT | 1 | 1 | B.6.6 | 0.000889 |
M | 196 | Y196Y | taC | taT | 1 | 1 | C.18 | 0.002591 |
M | 196 | Y196Y | taC | taT | 1 | 1 | C.35 | 0.000774 |
M | 196 | Y196Y | taC | taT | 1 | 1 | C.37 | 0.000116 |
M | 196 | Y196H | Tac | Cac | 1 | 1 | D.2 | 0.000075 |
M | 196 | Y196Y | taC | taT | 1 | 1 | L.2 | 0.011364 |
M | 196 | Y196Y | taC | taT | 1 | 1 | N.5 | 0.001767 |
M | 196 | Y196Y | taC | taT | 1 | 1 | P.1.10 | 0.000269 |
M | 196 | Y196Y | taC | taT | 1 | 1 | P.1.15 | 0.000232 |
M | 196 | Y196Y | taC | taT | 1 | 1 | P.1.4 | 0.000977 |
M | 196 | Y196Y | taC | taT | 1 | 1 | P.1.6 | 0.001946 |
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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