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 | 2 | F2L | nonsyn | ttT | ttA | 581 | 502 | 0.864028 | 21566-21568 | |
S | 2 | F2L | nonsyn | Ttt | Ctt | 581 | 72 | 0.123924 | 21566-21568 | |
S | 2 | F2L | nonsyn | ttT | ttG | 581 | 7 | 0.0120482 | 21566-21568 | |
S | 2 | F2S | nonsyn | tTt | tCt | 249 | 249 | 1 | 21566-21568 | |
S | 2 | F2del | del | TTT | --- | 51 | 51 | 1 | 21566-21568 | |
S | 2 | F2V | nonsyn | Ttt | Gtt | 32 | 32 | 1 | 21566-21568 | |
S | 2 | F2F | syn | ttT | ttC | 10 | 10 | 1 | 21566-21568 | |
S | 2 | F2I | nonsyn | Ttt | Att | 5 | 5 | 1 | 21566-21568 | |
S | 2 | F2C | nonsyn | tTt | tGt | 5 | 5 | 1 | 21566-21568 | |
S | 2 | F2Y | nonsyn | tTt | tAt | 2 | 2 | 1 | 21566-21568 | |
S | 2 | F2G | nonsyn | TTT | GGG | 1 | 1 | 1 | 21566-21568 | |
S | 2 | F2A | nonsyn | TTt | GCt | 1 | 1 | 1 | 21566-21568 | |
S | 2 | F2Q | nonsyn | TTT | CAA | 1 | 1 | 1 | 21566-21568 | |
S | 2 | F2del1 | del | Ttt | -tt | 1 | 1 | 1 | 21566-21568 | |
S | 2 | F2del2 | del | TTT | --N | 1 | 1 | 1 | 21566-21568 |
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 |
S | 2 | F2L | ttT | ttA | 502 | 581 | All | 0.000096 |
S | 2 | F2L | Ttt | Ctt | 72 | 581 | All | 0.000014 |
S | 2 | F2L | ttT | ttG | 7 | 581 | All | 0.000001 |
S | 2 | F2S | tTt | tCt | 249 | 249 | All | 0.000048 |
S | 2 | F2S | tTt | tCt | 223 | 223 | B.1.1.7 | 0.0002 |
S | 2 | F2L | ttT | ttA | 116 | 128 | B.1.1.7 | 0.000104 |
S | 2 | F2L | Ttt | Ctt | 12 | 128 | B.1.1.7 | 0.000011 |
S | 2 | F2L | ttT | ttA | 58 | 72 | B.1.2 | 0.000511 |
S | 2 | F2L | Ttt | Ctt | 13 | 72 | B.1.2 | 0.000114 |
S | 2 | F2L | ttT | ttG | 1 | 72 | B.1.2 | 0.000009 |
S | 2 | F2L | ttT | ttA | 54 | 54 | P.5 | 0.739726 |
S | 2 | F2del | TTT | --- | 51 | 51 | All | 0.00001 |
S | 2 | F2L | ttT | ttA | 33 | 33 | B.1.517 | 0.014091 |
S | 2 | F2V | Ttt | Gtt | 32 | 32 | All | 0.000006 |
S | 2 | F2L | ttT | ttA | 27 | 29 | B.1.258 | 0.001797 |
S | 2 | F2L | Ttt | Ctt | 2 | 29 | B.1.258 | 0.000133 |
S | 2 | F2V | Ttt | Gtt | 22 | 22 | B.1 | 0.000202 |
S | 2 | F2L | ttT | ttA | 19 | 21 | B.1.617.2 | 0.000072 |
S | 2 | F2L | Ttt | Ctt | 2 | 21 | B.1.617.2 | 0.000008 |
S | 2 | F2L | ttT | ttA | 17 | 19 | AY.43 | 0.000075 |
S | 2 | F2L | Ttt | Ctt | 2 | 19 | AY.43 | 0.000009 |
S | 2 | F2L | ttT | ttA | 18 | 18 | B.1.160 | 0.000561 |
S | 2 | F2L | ttT | ttA | 11 | 17 | AY.4 | 0.000017 |
S | 2 | F2L | Ttt | Ctt | 4 | 17 | AY.4 | 0.000006 |
S | 2 | F2L | ttT | ttG | 2 | 17 | AY.4 | 0.000003 |
S | 2 | F2L | ttT | ttA | 11 | 12 | B.1 | 0.000101 |
S | 2 | F2L | Ttt | Ctt | 1 | 12 | B.1 | 0.000009 |
S | 2 | F2F | ttT | ttC | 10 | 10 | All | 0.000002 |
S | 2 | F2L | ttT | ttA | 9 | 9 | AY.6 | 0.00037 |
S | 2 | F2L | ttT | ttA | 9 | 9 | B.1.1.519 | 0.000357 |
S | 2 | F2L | ttT | ttA | 6 | 8 | B.1.1 | 0.000109 |
S | 2 | F2L | Ttt | Ctt | 2 | 8 | B.1.1 | 0.000036 |
S | 2 | F2L | ttT | ttA | 7 | 7 | B | 0.000895 |
S | 2 | F2L | ttT | ttA | 5 | 6 | AY.103 | 0.000031 |
S | 2 | F2L | Ttt | Ctt | 1 | 6 | AY.103 | 0.000006 |
S | 2 | F2del | TTT | --- | 6 | 6 | AY.33 | 0.000401 |
S | 2 | F2L | ttT | ttA | 6 | 6 | AY.39.1 | 0.000238 |
S | 2 | F2L | ttT | ttA | 5 | 6 | B.1.429 | 0.000118 |
S | 2 | F2L | ttT | ttG | 1 | 6 | B.1.429 | 0.000024 |
S | 2 | F2L | ttT | ttA | 6 | 6 | B.1.577 | 0.004124 |
S | 2 | F2I | Ttt | Att | 5 | 5 | All | 0.000001 |
S | 2 | F2C | tTt | tGt | 5 | 5 | All | 0.000001 |
S | 2 | F2L | ttT | ttA | 5 | 5 | AY.34 | 0.000485 |
S | 2 | F2S | tTt | tCt | 5 | 5 | AY.4 | 0.000008 |
S | 2 | F2L | ttT | ttA | 3 | 5 | AY.44 | 0.000018 |
S | 2 | F2L | Ttt | Ctt | 1 | 5 | AY.44 | 0.000006 |
S | 2 | F2L | ttT | ttG | 1 | 5 | AY.44 | 0.000006 |
S | 2 | F2L | ttT | ttA | 5 | 5 | B.1.1.294 | 0.006329 |
S | 2 | F2L | ttT | ttA | 5 | 5 | B.1.448 | 0.013123 |
S | 2 | F2S | tTt | tCt | 5 | 5 | Q.8 | 0.000825 |
S | 2 | F2L | Ttt | Ctt | 3 | 4 | AY.39 | 0.000074 |
S | 2 | F2L | ttT | ttA | 1 | 4 | AY.39 | 0.000025 |
S | 2 | F2L | ttT | ttA | 4 | 4 | B.1.1.214 | 0.000222 |
S | 2 | F2del | TTT | --- | 4 | 4 | B.1.617.2 | 0.000015 |
S | 2 | F2del | TTT | --- | 3 | 3 | AY.25 | 0.000018 |
S | 2 | F2L | ttT | ttA | 3 | 3 | AY.3 | 0.00003 |
S | 2 | F2L | ttT | ttA | 3 | 3 | AY.33 | 0.0002 |
S | 2 | F2L | ttT | ttA | 3 | 3 | AY.4.2 | 0.000065 |
S | 2 | F2S | tTt | tCt | 3 | 3 | AY.4.2 | 0.000065 |
S | 2 | F2del | TTT | --- | 3 | 3 | AY.43 | 0.000013 |
S | 2 | F2F | ttT | ttC | 3 | 3 | B.1 | 0.000027 |
S | 2 | F2del | TTT | --- | 3 | 3 | B.1 | 0.000027 |
S | 2 | F2del | TTT | --- | 3 | 3 | B.1.1 | 0.000054 |
S | 2 | F2L | Ttt | Ctt | 3 | 3 | B.1.1.243 | 0.012245 |
S | 2 | F2del | TTT | --- | 3 | 3 | B.1.1.7 | 0.000003 |
S | 2 | F2L | Ttt | Ctt | 3 | 3 | B.1.139 | 0.002199 |
S | 2 | F2L | Ttt | Ctt | 2 | 3 | B.1.177 | 0.000026 |
S | 2 | F2L | ttT | ttA | 1 | 3 | B.1.177 | 0.000013 |
S | 2 | F2L | Ttt | Ctt | 3 | 3 | B.1.177.81 | 0.000568 |
S | 2 | F2S | tTt | tCt | 3 | 3 | B.1.427 | 0.000151 |
S | 2 | F2del | TTT | --- | 3 | 3 | P.1 | 0.000047 |
S | 2 | F2S | tTt | tCt | 2 | 2 | 0.111111 | |
S | 2 | F2Y | tTt | tAt | 2 | 2 | All | 0 |
S | 2 | F2L | ttT | ttA | 2 | 2 | AY.119 | 0.000071 |
S | 2 | F2L | ttT | ttA | 1 | 2 | AY.120 | 0.000037 |
S | 2 | F2L | Ttt | Ctt | 1 | 2 | AY.120 | 0.000037 |
S | 2 | F2L | Ttt | Ctt | 1 | 2 | AY.23 | 0.00007 |
S | 2 | F2L | ttT | ttA | 1 | 2 | AY.23 | 0.00007 |
S | 2 | F2L | Ttt | Ctt | 2 | 2 | AY.35 | 0.000466 |
S | 2 | F2L | ttT | ttA | 1 | 2 | AY.42 | 0.00004 |
S | 2 | F2L | ttT | ttG | 1 | 2 | AY.42 | 0.00004 |
S | 2 | F2L | ttT | ttA | 2 | 2 | AY.9 | 0.000135 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.1.207 | 0.002364 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.1.28 | 0.000622 |
S | 2 | F2V | Ttt | Gtt | 2 | 2 | B.1.1.33 | 0.000842 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.1.41 | 0.012658 |
S | 2 | F2del | TTT | --- | 2 | 2 | B.1.2 | 0.000018 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.351 | 0.000059 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.351.2 | 0.000605 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.427 | 0.000101 |
S | 2 | F2L | Ttt | Ctt | 1 | 2 | B.1.466.2 | 0.000391 |
S | 2 | F2L | ttT | ttA | 1 | 2 | B.1.466.2 | 0.000391 |
S | 2 | F2del | TTT | --- | 2 | 2 | B.1.525 | 0.000226 |
S | 2 | F2L | ttT | ttG | 1 | 2 | B.1.526 | 0.000024 |
S | 2 | F2L | ttT | ttA | 1 | 2 | B.1.526 | 0.000024 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.551 | 0.002581 |
S | 2 | F2L | ttT | ttA | 2 | 2 | B.1.617.1 | 0.000258 |
S | 2 | F2L | Ttt | Ctt | 2 | 2 | B.1.621 | 0.000177 |
S | 2 | F2L | ttT | ttA | 1 | 2 | P.1 | 0.000016 |
S | 2 | F2L | Ttt | Ctt | 1 | 2 | P.1 | 0.000016 |
S | 2 | F2V | Ttt | Gtt | 2 | 2 | P.2 | 0.000373 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | A.2.4 | 0.003367 |
S | 2 | F2del | TTT | --- | 1 | 1 | A.2.4 | 0.003367 |
S | 2 | F2L | ttT | ttA | 1 | 1 | A.2.5 | 0.000499 |
S | 2 | F2del2 | TTT | --N | 1 | 1 | All | 0 |
S | 2 | F2A | TTt | GCt | 1 | 1 | All | 0 |
S | 2 | F2Q | TTT | CAA | 1 | 1 | All | 0 |
S | 2 | F2del1 | Ttt | -tt | 1 | 1 | All | 0 |
S | 2 | F2G | TTT | GGG | 1 | 1 | All | 0 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AM.4 | 0.003571 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.100 | 0.000046 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.100 | 0.000046 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.102 | 0.000027 |
S | 2 | F2F | ttT | ttC | 1 | 1 | AY.103 | 0.000006 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.103 | 0.000006 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.116.1 | 0.000311 |
S | 2 | F2Y | tTt | tAt | 1 | 1 | AY.119 | 0.000035 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.121 | 0.000135 |
S | 2 | F2C | tTt | tGt | 1 | 1 | AY.13 | 0.000161 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.14 | 0.000088 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | AY.20 | 0.000039 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | AY.23.1 | 0.000417 |
S | 2 | F2S | tTt | tCt | 1 | 1 | AY.26 | 0.000028 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.26 | 0.000028 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.29 | 0.000016 |
S | 2 | F2V | Ttt | Gtt | 1 | 1 | AY.39 | 0.000025 |
S | 2 | F2F | ttT | ttC | 1 | 1 | AY.39 | 0.000025 |
S | 2 | F2I | Ttt | Att | 1 | 1 | AY.4 | 0.000002 |
S | 2 | F2F | ttT | ttC | 1 | 1 | AY.4 | 0.000002 |
S | 2 | F2I | Ttt | Att | 1 | 1 | AY.4.2 | 0.000022 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | AY.4.2.1 | 0.000149 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.4.3 | 0.000842 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.42 | 0.00004 |
S | 2 | F2F | ttT | ttC | 1 | 1 | AY.43 | 0.000004 |
S | 2 | F2V | Ttt | Gtt | 1 | 1 | AY.43 | 0.000004 |
S | 2 | F2I | Ttt | Att | 1 | 1 | AY.44 | 0.000006 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.46 | 0.000104 |
S | 2 | F2S | tTt | tCt | 1 | 1 | AY.46.5 | 0.000198 |
S | 2 | F2S | tTt | tCt | 1 | 1 | AY.46.6 | 0.000072 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.54 | 0.000095 |
S | 2 | F2del2 | TTT | --N | 1 | 1 | AY.59 | 0.00053 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.68 | 0.000274 |
S | 2 | F2L | ttT | ttA | 1 | 1 | AY.68 | 0.000274 |
S | 2 | F2F | ttT | ttC | 1 | 1 | AY.75 | 0.000056 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.85 | 0.000427 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | AY.9.1 | 0.000084 |
S | 2 | F2C | tTt | tGt | 1 | 1 | AY.91 | 0.00073 |
S | 2 | F2del | TTT | --- | 1 | 1 | AY.98 | 0.000079 |
S | 2 | F2S | tTt | tCt | 1 | 1 | B.1 | 0.000009 |
S | 2 | F2Y | tTt | tAt | 1 | 1 | B.1 | 0.000009 |
S | 2 | F2I | Ttt | Att | 1 | 1 | B.1.1 | 0.000018 |
S | 2 | F2S | tTt | tCt | 1 | 1 | B.1.1 | 0.000018 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.1.186 | 0.003436 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | B.1.1.25 | 0.000569 |
S | 2 | F2V | Ttt | Gtt | 1 | 1 | B.1.1.28 | 0.000311 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | B.1.1.284 | 0.000107 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.1.306 | 0.000438 |
S | 2 | F2del | TTT | --- | 1 | 1 | B.1.1.315 | 0.008475 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.1.318 | 0.000302 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.1.398 | 0.003226 |
S | 2 | F2del | TTT | --- | 1 | 1 | B.1.1.46 | 0.004367 |
S | 2 | F2S | tTt | tCt | 1 | 1 | B.1.157 | 0.002985 |
S | 2 | F2C | tTt | tGt | 1 | 1 | B.1.160 | 0.000031 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.160.8 | 0.001289 |
S | 2 | F2C | tTt | tGt | 1 | 1 | B.1.177 | 0.000013 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.177.4 | 0.000211 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.177.51 | 0.004566 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.177.54 | 0.000606 |
S | 2 | F2del | TTT | --- | 1 | 1 | B.1.177.68 | 0.015152 |
S | 2 | F2del | TTT | --- | 1 | 1 | B.1.177.83 | 0.001481 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.177.87 | 0.000728 |
S | 2 | F2F | ttT | ttC | 1 | 1 | B.1.2 | 0.000009 |
S | 2 | F2C | tTt | tGt | 1 | 1 | B.1.2 | 0.000009 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.221 | 0.000071 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.243 | 0.00007 |
S | 2 | F2del | TTT | --- | 1 | 1 | B.1.258.16 | 0.001637 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.268 | 0.010417 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.332 | 0.003497 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.36 | 0.000146 |
S | 2 | F2L | ttT | ttA | 1 | 1 | B.1.36.18 | 0.00042 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | B.1.396 | 0.000706 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | B.1.397 | 0.004854 |
S | 2 | F2A | TTt | GCt | 1 | 1 | B.1.416 | 0.001269 |
S | 2 | F2F | ttT | ttC | 1 | 1 | B.1.426 | 0.001009 |
S | 2 | F2del | TTT | --- | 1 | 1 | B.1.453 | 0.003236 |
S | 2 | F2V | Ttt | Gtt | 1 | 1 | B.1.528 | 0.047619 |
S | 2 | F2V | Ttt | Gtt | 1 | 1 | B.1.574 | 0.002151 |
S | 2 | F2del1 | Ttt | -tt | 1 | 1 | B.1.596 | 0.000087 |
S | 2 | F2L | Ttt | Ctt | 1 | 1 | B.1.609 | 0.000479 |
S | 2 | F2S | tTt | tCt | 1 | 1 | B.1.617.2 | 0.000004 |
S | 2 | F2I | Ttt | Att | 1 | 1 | B.1.617.2 | 0.000004 |
S | 2 | F2G | TTT | GGG | 1 | 1 | B.1.617.3 | 0.002985 |
S | 2 | F2del | TTT | --- | 1 | 1 | B.1.620 | 0.000946 |
S | 2 | F2S | tTt | tCt | 1 | 1 | B.1.637 | 0.000073 |
S | 2 | F2V | Ttt | Gtt | 1 | 1 | P.1 | 0.000016 |
S | 2 | F2Q | TTT | CAA | 1 | 1 | P.1 | 0.000016 |
S | 2 | F2del | TTT | --- | 1 | 1 | P.1.1 | 0.000318 |
S | 2 | F2del | TTT | --- | 1 | 1 | P.1.10 | 0.000269 |
S | 2 | F2del | TTT | --- | 1 | 1 | Q.8 | 0.000165 |
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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