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 | 221 | S221S | syn | tcG | tcA | 11997 | 1294 | 0.10786 | 22223-22225 |
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 | 221 | S221S | tcG | tcA | 1294 | 11997 | All | 0.000247 |
S | 221 | S221S | tcG | tcA | 230 | 2168 | B.1.1.7 | 0.000206 |
S | 221 | S221S | tcG | tcA | 62 | 1362 | AY.4 | 0.000096 |
S | 221 | S221S | tcG | tcA | 41 | 811 | B.1.617.2 | 0.000154 |
S | 221 | S221S | tcG | tcA | 65 | 458 | AY.44 | 0.000396 |
S | 221 | S221S | tcG | tcA | 19 | 456 | AY.43 | 0.000084 |
S | 221 | S221S | tcG | tcA | 39 | 423 | AY.26 | 0.001104 |
S | 221 | S221S | tcG | tcA | 2 | 366 | AY.5 | 0.000041 |
S | 221 | S221S | tcG | tcA | 15 | 363 | B.1.2 | 0.000132 |
S | 221 | S221S | tcG | tcA | 2 | 315 | AY.47 | 0.000062 |
S | 221 | S221S | tcG | tcA | 41 | 240 | B.1 | 0.000376 |
S | 221 | S221S | tcG | tcA | 179 | 194 | B.1.438.1 | 0.0192 |
S | 221 | S221S | tcG | tcA | 47 | 153 | AY.103 | 0.000292 |
S | 221 | S221S | tcG | tcA | 17 | 139 | AY.25 | 0.000102 |
S | 221 | S221S | tcG | tcA | 12 | 129 | AY.102 | 0.000318 |
S | 221 | S221S | tcG | tcA | 25 | 123 | P.1 | 0.000394 |
S | 221 | S221S | tcG | tcA | 1 | 105 | AY.6 | 0.000041 |
S | 221 | S221S | tcG | tcA | 8 | 103 | AY.61 | 0.000838 |
S | 221 | S221S | tcG | tcA | 35 | 103 | B.1.177 | 0.000461 |
S | 221 | S221S | tcG | tcA | 7 | 94 | B.1.1 | 0.000127 |
S | 221 | S221S | tcG | tcA | 3 | 94 | B.1.160 | 0.000094 |
S | 221 | S221S | tcG | tcA | 2 | 91 | AY.39 | 0.000049 |
S | 221 | S221S | tcG | tcA | 4 | 83 | AY.119 | 0.000141 |
S | 221 | S221S | tcG | tcA | 21 | 81 | AY.3 | 0.000209 |
S | 221 | S221S | tcG | tcA | 1 | 72 | B.1.1.70 | 0.000341 |
S | 221 | S221S | tcG | tcA | 12 | 66 | B.1.526 | 0.000282 |
S | 221 | S221S | tcG | tcA | 15 | 60 | B.1.258 | 0.000998 |
S | 221 | S221S | tcG | tcA | 1 | 57 | AY.98 | 0.000079 |
S | 221 | S221S | tcG | tcA | 49 | 56 | AY.76 | 0.236715 |
S | 221 | S221S | tcG | tcA | 3 | 46 | B.1.429 | 0.000071 |
S | 221 | S221S | tcG | tcA | 23 | 46 | B.1.596 | 0.002004 |
S | 221 | S221S | tcG | tcA | 4 | 42 | AY.20 | 0.000155 |
S | 221 | S221S | tcG | tcA | 2 | 41 | AY.33 | 0.000134 |
S | 221 | S221S | tcG | tcA | 6 | 40 | B.1.36 | 0.000875 |
S | 221 | S221S | tcG | tcA | 1 | 39 | AY.16 | 0.00038 |
S | 221 | S221S | tcG | tcA | 1 | 39 | AY.99.2 | 0.000092 |
S | 221 | S221S | tcG | tcA | 13 | 37 | AY.42 | 0.000523 |
S | 221 | S221S | tcG | tcA | 36 | 37 | B.1.36.36 | 0.021674 |
S | 221 | S221S | tcG | tcA | 28 | 35 | B.1.525 | 0.003168 |
S | 221 | S221S | tcG | tcA | 3 | 31 | AY.23 | 0.000209 |
S | 221 | S221S | tcG | tcA | 4 | 31 | AY.4.2 | 0.000087 |
S | 221 | S221S | tcG | tcA | 10 | 30 | AY.9 | 0.000676 |
S | 221 | S221S | tcG | tcA | 8 | 30 | B.1.1.519 | 0.000318 |
S | 221 | S221S | tcG | tcA | 1 | 29 | AY.120 | 0.000037 |
S | 221 | S221S | tcG | tcA | 9 | 29 | B.1.351 | 0.000268 |
S | 221 | S221S | tcG | tcA | 5 | 26 | B.1.243 | 0.000348 |
S | 221 | S221S | tcG | tcA | 6 | 25 | B.1.177.21 | 0.000459 |
S | 221 | S221S | tcG | tcA | 1 | 25 | B.1.36.29 | 0.000517 |
S | 221 | S221S | tcG | tcA | 1 | 24 | AY.13 | 0.000161 |
S | 221 | S221S | tcG | tcA | 3 | 24 | C.37 | 0.000348 |
S | 221 | S221S | tcG | tcA | 2 | 23 | B.1.221 | 0.000142 |
S | 221 | S221S | tcG | tcA | 5 | 21 | AY.29 | 0.000079 |
S | 221 | S221S | tcG | tcA | 6 | 21 | AY.98.1 | 0.000291 |
S | 221 | S221S | tcG | tcA | 3 | 18 | AY.100 | 0.000138 |
S | 221 | S221S | tcG | tcA | 11 | 18 | P.2 | 0.002053 |
S | 221 | S221S | tcG | tcA | 1 | 17 | AY.54 | 0.000095 |
S | 221 | S221S | tcG | tcA | 3 | 17 | B.1.177.60 | 0.000655 |
S | 221 | S221S | tcG | tcA | 13 | 15 | B.1.1.348 | 0.01035 |
S | 221 | S221S | tcG | tcA | 1 | 15 | P.1.14 | 0.000048 |
S | 221 | S221S | tcG | tcA | 2 | 14 | AY.39.1 | 0.000079 |
S | 221 | S221S | tcG | tcA | 14 | 14 | B.1.258.17 | 0.001456 |
S | 221 | S221S | tcG | tcA | 1 | 13 | AY.117 | 0.000085 |
S | 221 | S221S | tcG | tcA | 2 | 13 | AY.45 | 0.000243 |
S | 221 | S221S | tcG | tcA | 1 | 13 | AY.46 | 0.000104 |
S | 221 | S221S | tcG | tcA | 1 | 12 | AY.121 | 0.000135 |
S | 221 | S221S | tcG | tcA | 5 | 12 | B.1.311 | 0.001373 |
S | 221 | S221S | tcG | tcA | 2 | 11 | AY.59 | 0.001059 |
S | 221 | S221S | tcG | tcA | 11 | 11 | P.1.2 | 0.012717 |
S | 221 | S221S | tcG | tcA | 1 | 10 | B.1.1.222 | 0.000204 |
S | 221 | S221S | tcG | tcA | 1 | 10 | B.1.617.1 | 0.000129 |
S | 221 | S221S | tcG | tcA | 2 | 10 | Q.8 | 0.00033 |
S | 221 | S221S | tcG | tcA | 5 | 9 | AY.4.2.1 | 0.000745 |
S | 221 | S221S | tcG | tcA | 2 | 9 | AY.9.1 | 0.000167 |
S | 221 | S221S | tcG | tcA | 1 | 8 | B | 0.000128 |
S | 221 | S221S | tcG | tcA | 1 | 7 | AY.113 | 0.000142 |
S | 221 | S221S | tcG | tcA | 1 | 7 | AY.3.1 | 0.000085 |
S | 221 | S221S | tcG | tcA | 1 | 6 | AY.14 | 0.000088 |
S | 221 | S221S | tcG | tcA | 6 | 6 | C.26 | 0.044118 |
S | 221 | S221S | tcG | tcA | 1 | 5 | AY.46.4 | 0.000165 |
S | 221 | S221S | tcG | tcA | 2 | 5 | AY.69 | 0.000373 |
S | 221 | S221S | tcG | tcA | 5 | 5 | B.1.258.3 | 0.008375 |
S | 221 | S221S | tcG | tcA | 1 | 5 | P.1.15 | 0.000232 |
S | 221 | S221S | tcG | tcA | 1 | 5 | P.7 | 0.004367 |
S | 221 | S221S | tcG | tcA | 4 | 4 | B.1.221.2 | 0.016064 |
S | 221 | S221S | tcG | tcA | 1 | 4 | B.1.517 | 0.000427 |
S | 221 | S221S | tcG | tcA | 4 | 4 | Q.3 | 0.00058 |
S | 221 | S221S | tcG | tcA | 1 | 3 | A.23.1 | 0.000704 |
S | 221 | S221S | tcG | tcA | 1 | 3 | AY.106 | 0.000335 |
S | 221 | S221S | tcG | tcA | 3 | 3 | AY.28 | 0.005671 |
S | 221 | S221S | tcG | tcA | 3 | 3 | AY.91.1 | 0.012195 |
S | 221 | S221S | tcG | tcA | 3 | 3 | B.1.177.7 | 0.000495 |
S | 221 | S221S | tcG | tcA | 3 | 3 | B.1.233 | 0.042254 |
S | 221 | S221S | tcG | tcA | 1 | 3 | P.1.17 | 0.000162 |
S | 221 | S221S | tcG | tcA | 2 | 2 | A.28 | 0.005291 |
S | 221 | S221S | tcG | tcA | 1 | 2 | AY.29.1 | 0.000221 |
S | 221 | S221S | tcG | tcA | 1 | 2 | AY.7 | 0.000196 |
S | 221 | S221S | tcG | tcA | 1 | 2 | AY.88 | 0.000884 |
S | 221 | S221S | tcG | tcA | 2 | 2 | AY.94 | 0.000885 |
S | 221 | S221S | tcG | tcA | 1 | 2 | B.1.1.398 | 0.003226 |
S | 221 | S221S | tcG | tcA | 1 | 2 | B.1.400 | 0.000429 |
S | 221 | S221S | tcG | tcA | 2 | 2 | B.1.404 | 0.002604 |
S | 221 | S221S | tcG | tcA | 1 | 2 | Q.1 | 0.000126 |
S | 221 | S221S | tcG | tcA | 1 | 1 | A.21 | 0.00277 |
S | 221 | S221S | tcG | tcA | 1 | 1 | AY.10 | 0.00053 |
S | 221 | S221S | tcG | tcA | 1 | 1 | AY.4.1 | 0.000737 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.1.135 | 0.004695 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.1.157 | 0.000913 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.1.253 | 0.002506 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.1.294 | 0.001266 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.1.34 | 0.013158 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.177.35 | 0.000691 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.177.4 | 0.000211 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.333 | 0.010526 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.561 | 0.000397 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.567 | 0.003333 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.609 | 0.000479 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.623 | 0.000536 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.1.634 | 0.003425 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.3 | 0.000831 |
S | 221 | S221S | tcG | tcA | 1 | 1 | B.4.5 | 0.011905 |
S | 221 | S221S | tcG | tcA | 1 | 1 | C.14 | 0.004329 |
S | 221 | S221S | tcG | tcA | 1 | 1 | N.1 | 0.016949 |
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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