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 | 243 | A243S | nonsyn | Gct | Tct | 3898 | 3897 | 0.999743 | 22289-22291 | |
S | 243 | A243S | nonsyn | GcT | TcA | 3898 | 1 | 0.000256542 | 22289-22291 |
Details of the mutation A243S 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 | 243 | A243S | Gct | Tct | 3897 | 3898 | All | 0.000745 |
S | 243 | A243S | GcT | TcA | 1 | 3898 | All | 0 |
S | 243 | A243S | Gct | Tct | 950 | 950 | B.1.1.7 | 0.00085 |
S | 243 | A243S | Gct | Tct | 899 | 899 | AY.29 | 0.01418 |
S | 243 | A243S | Gct | Tct | 320 | 320 | AY.4 | 0.000498 |
S | 243 | A243S | Gct | Tct | 223 | 223 | AY.25 | 0.001341 |
S | 243 | A243S | Gct | Tct | 170 | 170 | B.1.429 | 0.004 |
S | 243 | A243S | Gct | Tct | 145 | 146 | AY.5 | 0.002994 |
S | 243 | A243S | GcT | TcA | 1 | 146 | AY.5 | 0.000021 |
S | 243 | A243S | Gct | Tct | 133 | 133 | B.1.525 | 0.01505 |
S | 243 | A243S | Gct | Tct | 82 | 82 | B.1.617.2 | 0.000309 |
S | 243 | A243S | Gct | Tct | 62 | 62 | P.1 | 0.000977 |
S | 243 | A243S | Gct | Tct | 57 | 57 | B.1.2 | 0.000502 |
S | 243 | A243S | Gct | Tct | 49 | 49 | AY.103 | 0.000304 |
S | 243 | A243S | Gct | Tct | 46 | 46 | AY.43 | 0.000204 |
S | 243 | A243S | Gct | Tct | 46 | 46 | B.1.139 | 0.033724 |
S | 243 | A243S | Gct | Tct | 45 | 45 | B.1 | 0.000412 |
S | 243 | A243S | Gct | Tct | 38 | 38 | AZ.5 | 0.133333 |
S | 243 | A243S | Gct | Tct | 31 | 31 | B.1.400 | 0.013299 |
S | 243 | A243S | Gct | Tct | 26 | 26 | B.1.582 | 0.012758 |
S | 243 | A243S | Gct | Tct | 24 | 24 | B.1.351.5 | 0.014388 |
S | 243 | A243S | Gct | Tct | 21 | 21 | AY.44 | 0.000128 |
S | 243 | A243S | Gct | Tct | 21 | 21 | B.1.1.519 | 0.000834 |
S | 243 | A243S | Gct | Tct | 20 | 20 | B.1.177 | 0.000263 |
S | 243 | A243S | Gct | Tct | 17 | 17 | B.1.427 | 0.000858 |
S | 243 | A243S | Gct | Tct | 16 | 16 | AY.120.1 | 0.005136 |
S | 243 | A243S | Gct | Tct | 14 | 14 | P.1.15 | 0.003253 |
S | 243 | A243S | Gct | Tct | 13 | 13 | B.1.1 | 0.000236 |
S | 243 | A243S | Gct | Tct | 13 | 13 | B.1.160 | 0.000405 |
S | 243 | A243S | Gct | Tct | 12 | 12 | B.1.526 | 0.000282 |
S | 243 | A243S | Gct | Tct | 11 | 11 | AY.114 | 0.002542 |
S | 243 | A243S | Gct | Tct | 11 | 11 | B.1.1.284 | 0.001181 |
S | 243 | A243S | Gct | Tct | 10 | 10 | AY.26 | 0.000283 |
S | 243 | A243S | Gct | Tct | 10 | 10 | AY.33 | 0.000668 |
S | 243 | A243S | Gct | Tct | 9 | 9 | AY.39 | 0.000222 |
S | 243 | A243S | Gct | Tct | 9 | 9 | AY.4.5 | 0.000967 |
S | 243 | A243S | Gct | Tct | 9 | 9 | B.1.214 | 0.032967 |
S | 243 | A243S | Gct | Tct | 9 | 9 | P.1.14 | 0.00043 |
S | 243 | A243S | Gct | Tct | 9 | 9 | Q.3 | 0.001305 |
S | 243 | A243S | Gct | Tct | 8 | 8 | AY.111 | 0.001465 |
S | 243 | A243S | Gct | Tct | 8 | 8 | AY.3 | 0.00008 |
S | 243 | A243S | Gct | Tct | 8 | 8 | AY.70 | 0.001668 |
S | 243 | A243S | Gct | Tct | 7 | 7 | AZ.2.1 | 0.056911 |
S | 243 | A243S | Gct | Tct | 6 | 6 | AY.102 | 0.000159 |
S | 243 | A243S | Gct | Tct | 6 | 6 | AY.42 | 0.000241 |
S | 243 | A243S | Gct | Tct | 6 | 6 | B.1.1.306 | 0.00263 |
S | 243 | A243S | Gct | Tct | 6 | 6 | B.1.265 | 0.007624 |
S | 243 | A243S | Gct | Tct | 6 | 6 | B.1.36.29 | 0.003104 |
S | 243 | A243S | Gct | Tct | 5 | 5 | AY.121 | 0.000677 |
S | 243 | A243S | Gct | Tct | 5 | 5 | AY.20 | 0.000194 |
S | 243 | A243S | Gct | Tct | 5 | 5 | AY.23 | 0.000349 |
S | 243 | A243S | Gct | Tct | 5 | 5 | AY.46 | 0.00052 |
S | 243 | A243S | Gct | Tct | 5 | 5 | AY.46.6 | 0.000361 |
S | 243 | A243S | Gct | Tct | 5 | 5 | B.1.1.277 | 0.003794 |
S | 243 | A243S | Gct | Tct | 5 | 5 | B.1.36.18 | 0.002101 |
S | 243 | A243S | Gct | Tct | 5 | 5 | B.1.568 | 0.005556 |
S | 243 | A243S | Gct | Tct | 5 | 5 | B.1.617.1 | 0.000645 |
S | 243 | A243S | Gct | Tct | 5 | 5 | C.37 | 0.00058 |
S | 243 | A243S | Gct | Tct | 4 | 4 | AY.106 | 0.00134 |
S | 243 | A243S | Gct | Tct | 4 | 4 | AY.113 | 0.00057 |
S | 243 | A243S | Gct | Tct | 4 | 4 | AY.29.1 | 0.000882 |
S | 243 | A243S | Gct | Tct | 4 | 4 | B.1.1.326 | 0.007042 |
S | 243 | A243S | Gct | Tct | 4 | 4 | B.1.240 | 0.000862 |
S | 243 | A243S | Gct | Tct | 4 | 4 | B.1.243 | 0.000278 |
S | 243 | A243S | Gct | Tct | 4 | 4 | B.1.565 | 0.003241 |
S | 243 | A243S | Gct | Tct | 4 | 4 | B.1.596 | 0.000349 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.120 | 0.000112 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.14 | 0.000264 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.39.1 | 0.000119 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.80 | 0.003386 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.87 | 0.002498 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.9.1 | 0.000251 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.90 | 0.002053 |
S | 243 | A243S | Gct | Tct | 3 | 3 | AY.98.1 | 0.000145 |
S | 243 | A243S | Gct | Tct | 3 | 3 | B.1.1.222 | 0.000612 |
S | 243 | A243S | Gct | Tct | 3 | 3 | B.1.1.318 | 0.000905 |
S | 243 | A243S | Gct | Tct | 3 | 3 | B.1.177.81 | 0.000568 |
S | 243 | A243S | Gct | Tct | 3 | 3 | B.1.241 | 0.002435 |
S | 243 | A243S | Gct | Tct | 3 | 3 | B.1.258 | 0.0002 |
S | 243 | A243S | Gct | Tct | 3 | 3 | B.1.351 | 0.000089 |
S | 243 | A243S | Gct | Tct | 3 | 3 | B.1.637 | 0.000219 |
S | 243 | A243S | Gct | Tct | 3 | 3 | Q.1 | 0.000379 |
S | 243 | A243S | Gct | Tct | 3 | 3 | Q.8 | 0.000495 |
S | 243 | A243S | Gct | Tct | 2 | 2 | A.1 | 0.000564 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.108 | 0.002205 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.119 | 0.000071 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.3.1 | 0.000171 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.34 | 0.000194 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.45 | 0.000243 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.6 | 0.000082 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.75 | 0.000112 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AY.93 | 0.000546 |
S | 243 | A243S | Gct | Tct | 2 | 2 | AZ.2 | 0.001642 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B | 0.000256 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.1.409 | 0.005666 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.177.14 | 0.012195 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.232 | 0.001075 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.239 | 0.002442 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.311 | 0.000549 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.36 | 0.000292 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.470 | 0.002809 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.538 | 0.016129 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.543 | 0.02 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.1.561 | 0.000794 |
S | 243 | A243S | Gct | Tct | 2 | 2 | B.6.6 | 0.001778 |
S | 243 | A243S | Gct | Tct | 2 | 2 | C.36 | 0.001821 |
S | 243 | A243S | Gct | Tct | 2 | 2 | P.1.7 | 0.000639 |
S | 243 | A243S | Gct | Tct | 1 | 1 | 0.055556 | |
S | 243 | A243S | Gct | Tct | 1 | 1 | A | 0.000387 |
S | 243 | A243S | Gct | Tct | 1 | 1 | A.29 | 0.005319 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AD.2 | 0.000219 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.109 | 0.00074 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.117 | 0.000085 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.16 | 0.00038 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.17 | 0.008197 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.36 | 0.000148 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.37 | 0.000316 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.38 | 0.000499 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.4.2 | 0.000022 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.4.2.1 | 0.000149 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.46.1 | 0.001027 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.46.5 | 0.000198 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.47 | 0.000031 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.54 | 0.000095 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.61 | 0.000105 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.67 | 0.000464 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.74 | 0.000116 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.77 | 0.001127 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.86 | 0.00083 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.9.2 | 0.000037 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.9.2.1 | 0.001976 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.92 | 0.000287 |
S | 243 | A243S | Gct | Tct | 1 | 1 | AY.99.2 | 0.000092 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.1 | 0.000327 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.214 | 0.000055 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.228 | 0.003049 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.269 | 0.001353 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.305 | 0.003861 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.317 | 0.000412 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.348 | 0.000796 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.427 | 0.142857 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.434 | 0.000349 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.525 | 0.005464 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.1.89 | 0.006061 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.111 | 0.001175 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.177.10 | 0.000878 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.177.44 | 0.000519 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.177.60 | 0.000218 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.177.66 | 0.041667 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.177.82 | 0.000477 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.206 | 0.000816 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.214.3 | 0.007143 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.23 | 0.006061 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.234 | 0.000132 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.258.17 | 0.000104 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.36.22 | 0.001208 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.36.26 | 0.002857 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.366 | 0.004878 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.367 | 0.000792 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.436 | 0.001029 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.459 | 0.004082 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.497 | 0.000315 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.499 | 0.00105 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.517 | 0.000427 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.541 | 0.004425 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.574 | 0.002151 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.595 | 0.000261 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.597 | 0.00463 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.621 | 0.000089 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.625 | 0.002353 |
S | 243 | A243S | Gct | Tct | 1 | 1 | B.1.632 | 0.006711 |
S | 243 | A243S | Gct | Tct | 1 | 1 | C.1 | 0.002392 |
S | 243 | A243S | Gct | Tct | 1 | 1 | C.16 | 0.00106 |
S | 243 | A243S | Gct | Tct | 1 | 1 | C.26 | 0.007353 |
S | 243 | A243S | Gct | Tct | 1 | 1 | C.8 | 0.004464 |
S | 243 | A243S | Gct | Tct | 1 | 1 | D.2 | 0.000075 |
S | 243 | A243S | Gct | Tct | 1 | 1 | P.1.17 | 0.000162 |
S | 243 | A243S | Gct | Tct | 1 | 1 | P.1.17.1 | 0.000875 |
S | 243 | A243S | Gct | Tct | 1 | 1 | P.2 | 0.000187 |
S | 243 | A243S | Gct | Tct | 1 | 1 | P.4 | 0.003802 |
S | 243 | A243S | Gct | Tct | 1 | 1 | Q.7 | 0.001111 |
S | 243 | A243S | Gct | Tct | 1 | 1 | R.1 | 0.00009 |
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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