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/nsp7 | 32 | C32C | C3891C | syn | tgT | tgC | 16741 | 16741 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32F | C3891F | nonsyn | tGt | tTt | 33 | 33 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32S | C3891S | nonsyn | Tgt | Agt | 22 | 17 | 0.772727 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32S | C3891S | nonsyn | tGt | tCt | 22 | 5 | 0.227273 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32del | C3891del | del | TGT | --- | 9 | 9 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32Y | C3891Y | nonsyn | tGt | tAt | 6 | 6 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32del1 | C3891del1 | del | Tgt | -gt | 6 | 6 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32R | C3891R | nonsyn | Tgt | Cgt | 3 | 3 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32del2 | C3891del2 | del | TGt | --t | 2 | 2 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32G | C3891G | nonsyn | Tgt | Ggt | 1 | 1 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32W | C3891W | nonsyn | tgT | tgG | 1 | 1 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32X | C3891X | nonsyn | tGT | tAA | 1 | 1 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32I | C3891I | nonsyn | TGt | ATt | 1 | 1 | 1 | 11936-11938 |
ORF1ab/nsp7 | 32 | C32T | C3891T | nonsyn | TGt | ACt | 1 | 1 | 1 | 11936-11938 |
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/nsp7 | 32 | C32C | tgT | tgC | 16741 | 16741 | All | 0.003202 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 15375 | 15375 | AY.27 | 0.995081 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 447 | 447 | B.1.617.2 | 0.001683 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 158 | 158 | AY.61 | 0.016555 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 139 | 139 | C.23 | 0.80814 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 94 | 94 | B.1.1.317 | 0.038699 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 69 | 69 | AY.37 | 0.021808 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 60 | 60 | B.1.1 | 0.001088 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 45 | 45 | AY.25 | 0.000271 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 33 | 33 | All | 0.000006 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 33 | 33 | AY.75.1 | 0.00595 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 33 | 33 | B.1.1.7 | 0.00003 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 28 | 28 | B.1 | 0.000256 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 25 | 25 | AY.4 | 0.000039 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 24 | 24 | AY.19 | 0.027366 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 24 | 24 | AY.44 | 0.000146 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 17 | 22 | All | 0.000003 |
ORF1ab/nsp7 | 32 | C32S | tGt | tCt | 5 | 22 | All | 0.000001 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 17 | 17 | AY.16 | 0.006454 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 15 | 15 | AY.74 | 0.001735 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 14 | 14 | AY.26 | 0.000396 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 11 | 11 | AY.13 | 0.001771 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 9 | 9 | All | 0.000002 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 9 | 9 | AY.16.1 | 0.004229 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 9 | 9 | AY.47 | 0.00028 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 9 | 9 | B.1.1.1 | 0.00294 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 9 | 9 | B.1.2 | 0.000079 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 7 | 7 | AY.103 | 0.000043 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 7 | 7 | AY.62 | 0.00305 |
ORF1ab/nsp7 | 32 | C32Y | tGt | tAt | 6 | 6 | All | 0.000001 |
ORF1ab/nsp7 | 32 | C32del1 | Tgt | -gt | 6 | 6 | All | 0.000001 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 6 | 6 | AY.110 | 0.000676 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 5 | 5 | AY.43 | 0.000022 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 5 | 5 | AY.44 | 0.00003 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 5 | 5 | AY.5 | 0.000103 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 3 | 5 | B.1.1.7 | 0.000003 |
ORF1ab/nsp7 | 32 | C32S | tGt | tCt | 2 | 5 | B.1.1.7 | 0.000002 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 4 | 4 | AY.43 | 0.000018 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 4 | 4 | AY.75 | 0.000224 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 4 | 4 | AY.9.2 | 0.000147 |
ORF1ab/nsp7 | 32 | C32R | Tgt | Cgt | 3 | 3 | All | 0.000001 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 3 | 3 | AY.39 | 0.000074 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 3 | 3 | AY.55 | 0.002752 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 3 | 3 | AY.65 | 0.001599 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 3 | 3 | AY.66 | 0.003209 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 3 | 3 | AY.67 | 0.001393 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 3 | 3 | B.1.1.7 | 0.000003 |
ORF1ab/nsp7 | 32 | C32del2 | TGt | --t | 2 | 2 | All | 0 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp7 | 32 | C32del1 | Tgt | -gt | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | AY.33 | 0.000134 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | AY.42 | 0.00008 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 2 | 2 | AY.5 | 0.000041 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | AY.60 | 0.001876 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | AY.68 | 0.000547 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 2 | 2 | AY.71 | 0.00095 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | AY.71 | 0.00095 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 2 | 2 | AY.98.1 | 0.000097 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 1 | 2 | B.1.1 | 0.000018 |
ORF1ab/nsp7 | 32 | C32S | tGt | tCt | 1 | 2 | B.1.1 | 0.000018 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 2 | 2 | B.1.2 | 0.000018 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | B.1.236 | 0.004107 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 2 | 2 | P.1.17 | 0.000324 |
ORF1ab/nsp7 | 32 | C32Y | tGt | tAt | 1 | 1 | A | 0.000387 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | A | 0.000387 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | A.2 | 0.000662 |
ORF1ab/nsp7 | 32 | C32I | TGt | ATt | 1 | 1 | All | 0 |
ORF1ab/nsp7 | 32 | C32T | TGt | ACt | 1 | 1 | All | 0 |
ORF1ab/nsp7 | 32 | C32G | Tgt | Ggt | 1 | 1 | All | 0 |
ORF1ab/nsp7 | 32 | C32W | tgT | tgG | 1 | 1 | All | 0 |
ORF1ab/nsp7 | 32 | C32X | tGT | tAA | 1 | 1 | All | 0 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.10 | 0.00053 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp7 | 32 | C32del1 | Tgt | -gt | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp7 | 32 | C32X | tGT | tAA | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp7 | 32 | C32del1 | Tgt | -gt | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.49 | 0.003195 |
ORF1ab/nsp7 | 32 | C32del1 | Tgt | -gt | 1 | 1 | AY.5.3 | 0.000337 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp7 | 32 | C32Y | tGt | tAt | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.69 | 0.000187 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.79 | 0.001211 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp7 | 32 | C32R | Tgt | Cgt | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | AY.93 | 0.000273 |
ORF1ab/nsp7 | 32 | C32G | Tgt | Ggt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp7 | 32 | C32I | TGt | ATt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp7 | 32 | C32T | TGt | ACt | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.1.220 | 0.001859 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.1.1.356 | 0.008547 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.1.1.433 | 0.001425 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 1 | 1 | B.1.1.448 | 0.002033 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.1.464 | 0.001473 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.1.50 | 0.000679 |
ORF1ab/nsp7 | 32 | C32R | Tgt | Cgt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp7 | 32 | C32del1 | Tgt | -gt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.1.1.8 | 0.003584 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.143 | 0.021277 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp7 | 32 | C32Y | tGt | tAt | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp7 | 32 | C32Y | tGt | tAt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp7 | 32 | C32del2 | TGt | --t | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp7 | 32 | C32S | Tgt | Agt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp7 | 32 | C32W | tgT | tgG | 1 | 1 | B.1.39 | 0.003906 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 1 | 1 | B.1.415 | 0.014286 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.470 | 0.001404 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.576 | 0.000907 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.604 | 0.017241 |
ORF1ab/nsp7 | 32 | C32C | tgT | tgC | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp7 | 32 | C32S | tGt | tCt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp7 | 32 | C32Y | tGt | tAt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp7 | 32 | C32del2 | TGt | --t | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp7 | 32 | C32Y | tGt | tAt | 1 | 1 | B.4.4 | 0.018868 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.4.5 | 0.011905 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | B.6 | 0.00091 |
ORF1ab/nsp7 | 32 | C32S | tGt | tCt | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp7 | 32 | C32F | tGt | tTt | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 1 | 1 | N.4 | 0.004255 |
ORF1ab/nsp7 | 32 | C32R | Tgt | Cgt | 1 | 1 | P.1.7 | 0.000319 |
ORF1ab/nsp7 | 32 | C32del | TGT | --- | 1 | 1 | Q.2 | 0.000613 |
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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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