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 | 653 | A653V | nonsyn | gCt | gTt | 8238 | 8211 | 0.996723 | 23519-23521 | |
S | 653 | A653V | nonsyn | gCT | gTA | 8238 | 19 | 0.00230638 | 23519-23521 | |
S | 653 | A653V | nonsyn | gCT | gTC | 8238 | 8 | 0.000971109 | 23519-23521 |
Details of the mutation A653V 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 | 653 | A653V | gCt | gTt | 8211 | 8238 | All | 0.00157 |
S | 653 | A653V | gCT | gTA | 19 | 8238 | All | 0.000004 |
S | 653 | A653V | gCT | gTC | 8 | 8238 | All | 0.000002 |
S | 653 | A653V | gCt | gTt | 2943 | 2960 | B.1.1.7 | 0.002635 |
S | 653 | A653V | gCT | gTA | 17 | 2960 | B.1.1.7 | 0.000015 |
S | 653 | A653V | gCt | gTt | 1785 | 1785 | B.1.438.1 | 0.191462 |
S | 653 | A653V | gCt | gTt | 584 | 584 | A.27 | 0.966887 |
S | 653 | A653V | gCt | gTt | 347 | 347 | AY.4 | 0.00054 |
S | 653 | A653V | gCt | gTt | 299 | 301 | AY.3 | 0.002974 |
S | 653 | A653V | gCT | gTC | 2 | 301 | AY.3 | 0.00002 |
S | 653 | A653V | gCt | gTt | 209 | 209 | AY.20 | 0.008123 |
S | 653 | A653V | gCt | gTt | 170 | 170 | AY.103 | 0.001056 |
S | 653 | A653V | gCt | gTt | 155 | 157 | P.1 | 0.002442 |
S | 653 | A653V | gCT | gTA | 2 | 157 | P.1 | 0.000032 |
S | 653 | A653V | gCt | gTt | 138 | 138 | AY.25 | 0.00083 |
S | 653 | A653V | gCt | gTt | 102 | 102 | B.1.526 | 0.002397 |
S | 653 | A653V | gCt | gTt | 96 | 98 | B.1.617.2 | 0.000361 |
S | 653 | A653V | gCT | gTC | 2 | 98 | B.1.617.2 | 0.000008 |
S | 653 | A653V | gCt | gTt | 91 | 91 | B.1.2 | 0.000801 |
S | 653 | A653V | gCt | gTt | 83 | 83 | B.1.351 | 0.002467 |
S | 653 | A653V | gCt | gTt | 53 | 53 | AY.26 | 0.0015 |
S | 653 | A653V | gCt | gTt | 50 | 50 | AY.116.1 | 0.015571 |
S | 653 | A653V | gCt | gTt | 50 | 50 | B.1 | 0.000458 |
S | 653 | A653V | gCt | gTt | 47 | 47 | P.1.7 | 0.015006 |
S | 653 | A653V | gCt | gTt | 39 | 39 | AY.120.1 | 0.01252 |
S | 653 | A653V | gCt | gTt | 37 | 38 | AY.43 | 0.000164 |
S | 653 | A653V | gCT | gTC | 1 | 38 | AY.43 | 0.000004 |
S | 653 | A653V | gCt | gTt | 36 | 36 | AY.5 | 0.000743 |
S | 653 | A653V | gCt | gTt | 36 | 36 | W.4 | 0.048649 |
S | 653 | A653V | gCt | gTt | 31 | 31 | B.1.177 | 0.000408 |
S | 653 | A653V | gCt | gTt | 29 | 29 | AY.44 | 0.000177 |
S | 653 | A653V | gCt | gTt | 29 | 29 | B.1.1 | 0.000526 |
S | 653 | A653V | gCt | gTt | 29 | 29 | B.1.160 | 0.000904 |
S | 653 | A653V | gCt | gTt | 28 | 28 | P.4 | 0.106464 |
S | 653 | A653V | gCt | gTt | 24 | 24 | B.1.1.519 | 0.000953 |
S | 653 | A653V | gCt | gTt | 23 | 23 | AY.39.1 | 0.000911 |
S | 653 | A653V | gCt | gTt | 23 | 23 | AY.6 | 0.000946 |
S | 653 | A653V | gCt | gTt | 19 | 19 | B.1.36.9 | 0.061093 |
S | 653 | A653V | gCt | gTt | 16 | 16 | A | 0.006192 |
S | 653 | A653V | gCt | gTt | 16 | 16 | AY.36 | 0.002371 |
S | 653 | A653V | gCt | gTt | 15 | 15 | B.1.36.31 | 0.02627 |
S | 653 | A653V | gCt | gTt | 15 | 15 | B.1.429 | 0.000353 |
S | 653 | A653V | gCt | gTt | 15 | 15 | P.1.17 | 0.002426 |
S | 653 | A653V | gCt | gTt | 14 | 14 | B.1.637 | 0.001023 |
S | 653 | A653V | gCt | gTt | 12 | 12 | B | 0.001534 |
S | 653 | A653V | gCt | gTt | 11 | 11 | AY.39 | 0.000272 |
S | 653 | A653V | gCt | gTt | 11 | 11 | AY.4.2 | 0.000239 |
S | 653 | A653V | gCt | gTt | 11 | 11 | B.1.1.84 | 1 |
S | 653 | A653V | gCt | gTt | 11 | 11 | B.1.177.21 | 0.000841 |
S | 653 | A653V | gCt | gTt | 11 | 11 | B.1.562 | 0.203704 |
S | 653 | A653V | gCt | gTt | 11 | 11 | Q.8 | 0.001814 |
S | 653 | A653V | gCt | gTt | 10 | 10 | AY.29 | 0.000158 |
S | 653 | A653V | gCt | gTt | 10 | 10 | B.1.1.1 | 0.003267 |
S | 653 | A653V | gCt | gTt | 10 | 10 | B.1.243 | 0.000696 |
S | 653 | A653V | gCt | gTt | 10 | 10 | B.1.258 | 0.000665 |
S | 653 | A653V | gCt | gTt | 10 | 10 | B.1.258.14 | 0.009804 |
S | 653 | A653V | gCt | gTt | 10 | 10 | C.16 | 0.010604 |
S | 653 | A653V | gCt | gTt | 9 | 9 | AY.101 | 0.004414 |
S | 653 | A653V | gCt | gTt | 8 | 9 | AY.102 | 0.000212 |
S | 653 | A653V | gCT | gTC | 1 | 9 | AY.102 | 0.000027 |
S | 653 | A653V | gCt | gTt | 9 | 9 | B.1.1.284 | 0.000967 |
S | 653 | A653V | gCt | gTt | 9 | 9 | C.37 | 0.001045 |
S | 653 | A653V | gCt | gTt | 9 | 9 | P.1.14 | 0.00043 |
S | 653 | A653V | gCt | gTt | 9 | 9 | P.1.15 | 0.002091 |
S | 653 | A653V | gCt | gTt | 9 | 9 | Q.1 | 0.001137 |
S | 653 | A653V | gCt | gTt | 8 | 8 | AY.111 | 0.001465 |
S | 653 | A653V | gCt | gTt | 8 | 8 | AY.35 | 0.001864 |
S | 653 | A653V | gCt | gTt | 8 | 8 | B.1.177.9 | 0.010652 |
S | 653 | A653V | gCt | gTt | 8 | 8 | B.1.221 | 0.000568 |
S | 653 | A653V | gCt | gTt | 8 | 8 | B.1.258.17 | 0.000832 |
S | 653 | A653V | gCt | gTt | 7 | 7 | AY.120 | 0.00026 |
S | 653 | A653V | gCt | gTt | 7 | 7 | B.1.258.11 | 0.002774 |
S | 653 | A653V | gCt | gTt | 7 | 7 | B.1.349 | 0.005004 |
S | 653 | A653V | gCt | gTt | 7 | 7 | B.1.596 | 0.00061 |
S | 653 | A653V | gCt | gTt | 6 | 6 | AY.119 | 0.000212 |
S | 653 | A653V | gCt | gTt | 6 | 6 | AY.23 | 0.000418 |
S | 653 | A653V | gCt | gTt | 6 | 6 | AY.33 | 0.000401 |
S | 653 | A653V | gCt | gTt | 6 | 6 | AY.99.2 | 0.000553 |
S | 653 | A653V | gCt | gTt | 5 | 5 | B.1.427 | 0.000252 |
S | 653 | A653V | gCt | gTt | 5 | 5 | B.1.478 | 0.058824 |
S | 653 | A653V | gCt | gTt | 4 | 4 | A.2.5 | 0.001996 |
S | 653 | A653V | gCt | gTt | 3 | 4 | AY.113 | 0.000427 |
S | 653 | A653V | gCT | gTC | 1 | 4 | AY.113 | 0.000142 |
S | 653 | A653V | gCt | gTt | 4 | 4 | AY.117 | 0.000338 |
S | 653 | A653V | gCt | gTt | 4 | 4 | AY.4.4 | 0.001637 |
S | 653 | A653V | gCt | gTt | 4 | 4 | AY.45 | 0.000487 |
S | 653 | A653V | gCt | gTt | 4 | 4 | AY.68 | 0.001095 |
S | 653 | A653V | gCt | gTt | 4 | 4 | AY.69 | 0.000747 |
S | 653 | A653V | gCt | gTt | 4 | 4 | AY.75 | 0.000224 |
S | 653 | A653V | gCt | gTt | 4 | 4 | B.1.1.33 | 0.001684 |
S | 653 | A653V | gCt | gTt | 4 | 4 | B.1.177.77 | 0.002905 |
S | 653 | A653V | gCt | gTt | 4 | 4 | B.1.525 | 0.000453 |
S | 653 | A653V | gCt | gTt | 4 | 4 | B.1.568 | 0.004444 |
S | 653 | A653V | gCt | gTt | 4 | 4 | D.2 | 0.0003 |
S | 653 | A653V | gCt | gTt | 3 | 3 | A.29 | 0.015957 |
S | 653 | A653V | gCt | gTt | 3 | 3 | AY.46.4 | 0.000494 |
S | 653 | A653V | gCt | gTt | 3 | 3 | AY.70 | 0.000626 |
S | 653 | A653V | gCt | gTt | 3 | 3 | AY.75.1 | 0.000541 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.1.1.214 | 0.000166 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.1.1.222 | 0.000612 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.1.1.25 | 0.001706 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.1.36.36 | 0.001806 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.1.367 | 0.002377 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.1.369 | 0.000856 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.1.438 | 0.019608 |
S | 653 | A653V | gCt | gTt | 3 | 3 | B.6.6 | 0.002667 |
S | 653 | A653V | gCt | gTt | 3 | 3 | P.1.16 | 0.001122 |
S | 653 | A653V | gCt | gTt | 3 | 3 | Q.3 | 0.000435 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AD.2 | 0.000438 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.106 | 0.00067 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.12 | 0.000632 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.16.1 | 0.00094 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.27 | 0.000129 |
S | 653 | A653V | gCT | gTC | 1 | 2 | AY.46.6 | 0.000072 |
S | 653 | A653V | gCt | gTt | 1 | 2 | AY.46.6 | 0.000072 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.5.3 | 0.000675 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.5.4 | 0.000553 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.98 | 0.000158 |
S | 653 | A653V | gCt | gTt | 2 | 2 | AY.98.1 | 0.000097 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.1.10 | 0.00223 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.1.159 | 0.009346 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.1.28 | 0.000622 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.1.376 | 0.011905 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.160.16 | 0.001859 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.162 | 0.01005 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.177.4 | 0.000422 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.177.60 | 0.000437 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.177.81 | 0.000379 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.177.83 | 0.002963 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.332 | 0.006993 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.36.39 | 0.004435 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.396 | 0.001411 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.400 | 0.000858 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.433 | 0.00639 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.582 | 0.000981 |
S | 653 | A653V | gCt | gTt | 2 | 2 | B.1.595 | 0.000522 |
S | 653 | A653V | gCt | gTt | 2 | 2 | P.2 | 0.000373 |
S | 653 | A653V | gCt | gTt | 2 | 2 | R.1 | 0.00018 |
S | 653 | A653V | gCt | gTt | 1 | 1 | A.1 | 0.000282 |
S | 653 | A653V | gCt | gTt | 1 | 1 | A.2 | 0.000662 |
S | 653 | A653V | gCt | gTt | 1 | 1 | A.22 | 0.066667 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AS.1 | 0.009524 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AU.3 | 0.00211 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.100 | 0.000046 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.110 | 0.000113 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.114 | 0.000231 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.16 | 0.00038 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.19 | 0.00114 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.24 | 0.000431 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.32 | 0.000532 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.39.1.1 | 0.000725 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.4.5 | 0.000107 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.42 | 0.00004 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.47 | 0.000031 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.51 | 0.000909 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.58 | 0.000907 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.64 | 0.000595 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.67 | 0.000464 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.85 | 0.000427 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.9 | 0.000068 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.92 | 0.000287 |
S | 653 | A653V | gCt | gTt | 1 | 1 | AY.99.1 | 0.001553 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.153 | 0.001095 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.161 | 0.003534 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.174 | 0.003378 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.191 | 0.004762 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.207 | 0.001182 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.269 | 0.001353 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.291 | 0.000742 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.348 | 0.000796 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.374 | 0.002375 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.377 | 0.001381 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.409 | 0.002833 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.420 | 0.001006 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.44 | 0.00241 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.57 | 0.011494 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.1.70 | 0.000341 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.126 | 0.001276 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.160.21 | 0.020408 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.160.33 | 0.004425 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.177.11 | 0.001698 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.177.15 | 0.000631 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.177.16 | 0.000664 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.177.31 | 0.011494 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.177.32 | 0.00135 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.177.53 | 0.002392 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.177.86 | 0.000183 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.232 | 0.000537 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.234 | 0.000132 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.240 | 0.000216 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.264 | 0.012346 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.302 | 0.013333 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.337 | 0.005587 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.351.2 | 0.000303 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.351.3 | 0.000876 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.36 | 0.000146 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.362 | 0.001541 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.416 | 0.001269 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.422 | 0.000812 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.497 | 0.000315 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.575 | 0.000303 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.576 | 0.000907 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.597 | 0.00463 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.617.1 | 0.000129 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.617.3 | 0.002985 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.619.1 | 0.000641 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.621 | 0.000089 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.621.1 | 0.000506 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.1.9.5 | 0.005682 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.3 | 0.000831 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.39 | 0.002331 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.4 | 0.002208 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.40 | 0.000364 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.55 | 0.00295 |
S | 653 | A653V | gCt | gTt | 1 | 1 | B.58 | 0.010204 |
S | 653 | A653V | gCt | gTt | 1 | 1 | C.6 | 0.037037 |
S | 653 | A653V | gCt | gTt | 1 | 1 | P.1.10 | 0.000269 |
S | 653 | A653V | gCt | gTt | 1 | 1 | P.1.12 | 0.000484 |
S | 653 | A653V | gCt | gTt | 1 | 1 | P.1.2 | 0.001156 |
S | 653 | A653V | gCt | gTt | 1 | 1 | P.1.4 | 0.000977 |
S | 653 | A653V | gCt | gTt | 1 | 1 | P.6 | 0.003145 |
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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