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 | 222 | A222S | nonsyn | Gct | Tct | 3190 | 3187 | 0.99906 | 22226-22228 | |
S | 222 | A222S | nonsyn | GcT | TcA | 3190 | 2 | 0.000626959 | 22226-22228 | |
S | 222 | A222S | nonsyn | GcT | TcG | 3190 | 1 | 0.00031348 | 22226-22228 |
Details of the mutation A222S 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 | 222 | A222S | Gct | Tct | 3187 | 3190 | All | 0.00061 |
S | 222 | A222S | GcT | TcA | 2 | 3190 | All | 0 |
S | 222 | A222S | GcT | TcG | 1 | 3190 | All | 0 |
S | 222 | A222S | Gct | Tct | 626 | 626 | AY.46.4 | 0.102977 |
S | 222 | A222S | Gct | Tct | 559 | 559 | AY.4 | 0.00087 |
S | 222 | A222S | Gct | Tct | 370 | 370 | B.1.1.7 | 0.000331 |
S | 222 | A222S | Gct | Tct | 214 | 214 | B.1.617.2 | 0.000806 |
S | 222 | A222S | Gct | Tct | 157 | 157 | AY.43 | 0.000696 |
S | 222 | A222S | Gct | Tct | 124 | 124 | B.1.637 | 0.009061 |
S | 222 | A222S | Gct | Tct | 97 | 97 | AY.25 | 0.000583 |
S | 222 | A222S | Gct | Tct | 90 | 90 | AY.44 | 0.000548 |
S | 222 | A222S | Gct | Tct | 81 | 81 | AY.103 | 0.000503 |
S | 222 | A222S | Gct | Tct | 77 | 77 | AY.102 | 0.002042 |
S | 222 | A222S | Gct | Tct | 74 | 74 | AY.99.2 | 0.00682 |
S | 222 | A222S | Gct | Tct | 66 | 66 | P.1.14 | 0.003155 |
S | 222 | A222S | Gct | Tct | 64 | 64 | AY.39 | 0.001582 |
S | 222 | A222S | Gct | Tct | 42 | 42 | AY.3 | 0.000418 |
S | 222 | A222S | Gct | Tct | 34 | 34 | AY.3.1 | 0.002899 |
S | 222 | A222S | Gct | Tct | 27 | 27 | AY.101 | 0.013242 |
S | 222 | A222S | Gct | Tct | 27 | 27 | AY.119 | 0.000953 |
S | 222 | A222S | Gct | Tct | 25 | 25 | AY.20 | 0.000972 |
S | 222 | A222S | Gct | Tct | 21 | 21 | B.1.2 | 0.000185 |
S | 222 | A222S | Gct | Tct | 20 | 20 | AY.118 | 0.001253 |
S | 222 | A222S | Gct | Tct | 19 | 19 | AY.33 | 0.001269 |
S | 222 | A222S | Gct | Tct | 19 | 19 | AY.46.6 | 0.001372 |
S | 222 | A222S | Gct | Tct | 17 | 19 | P.1 | 0.000268 |
S | 222 | A222S | GcT | TcG | 1 | 19 | P.1 | 0.000016 |
S | 222 | A222S | GcT | TcA | 1 | 19 | P.1 | 0.000016 |
S | 222 | A222S | Gct | Tct | 18 | 18 | AY.42 | 0.000724 |
S | 222 | A222S | Gct | Tct | 16 | 16 | AY.29 | 0.000252 |
S | 222 | A222S | Gct | Tct | 15 | 15 | AY.110 | 0.00169 |
S | 222 | A222S | Gct | Tct | 14 | 14 | B.1 | 0.000128 |
S | 222 | A222S | Gct | Tct | 12 | 12 | AY.34 | 0.001164 |
S | 222 | A222S | Gct | Tct | 12 | 12 | AY.5 | 0.000248 |
S | 222 | A222S | Gct | Tct | 11 | 11 | AY.100 | 0.000506 |
S | 222 | A222S | Gct | Tct | 11 | 11 | AY.120 | 0.000409 |
S | 222 | A222S | Gct | Tct | 11 | 11 | AY.46 | 0.001145 |
S | 222 | A222S | Gct | Tct | 10 | 10 | AY.4.3 | 0.008418 |
S | 222 | A222S | Gct | Tct | 8 | 8 | AY.6 | 0.000329 |
S | 222 | A222S | Gct | Tct | 8 | 8 | B.1.1.519 | 0.000318 |
S | 222 | A222S | Gct | Tct | 8 | 8 | B.1.526 | 0.000188 |
S | 222 | A222S | Gct | Tct | 7 | 7 | AY.113 | 0.000997 |
S | 222 | A222S | Gct | Tct | 7 | 7 | AY.117 | 0.000592 |
S | 222 | A222S | Gct | Tct | 7 | 7 | B.1.36.39 | 0.015521 |
S | 222 | A222S | Gct | Tct | 6 | 6 | AY.4.5 | 0.000645 |
S | 222 | A222S | Gct | Tct | 6 | 6 | AY.88 | 0.005305 |
S | 222 | A222S | Gct | Tct | 6 | 6 | Q.8 | 0.000989 |
S | 222 | A222S | Gct | Tct | 5 | 5 | AY.116.1 | 0.001557 |
S | 222 | A222S | Gct | Tct | 5 | 5 | AY.91 | 0.003652 |
S | 222 | A222S | Gct | Tct | 5 | 5 | B.1.525 | 0.000566 |
S | 222 | A222S | Gct | Tct | 4 | 4 | AY.116 | 0.001147 |
S | 222 | A222S | Gct | Tct | 4 | 4 | AY.51 | 0.003636 |
S | 222 | A222S | Gct | Tct | 4 | 4 | AY.98 | 0.000316 |
S | 222 | A222S | Gct | Tct | 4 | 4 | B.1.36.29 | 0.002069 |
S | 222 | A222S | Gct | Tct | 4 | 4 | B.1.429 | 0.000094 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.106 | 0.001005 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.120.1 | 0.000963 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.121 | 0.000406 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.23 | 0.000209 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.41 | 0.000882 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.54 | 0.000286 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.7.2 | 0.001678 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.85 | 0.001282 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.9.2 | 0.00011 |
S | 222 | A222S | Gct | Tct | 3 | 3 | AY.98.1 | 0.000145 |
S | 222 | A222S | Gct | Tct | 3 | 3 | B.1.524 | 0.004219 |
S | 222 | A222S | Gct | Tct | 3 | 3 | C.37 | 0.000348 |
S | 222 | A222S | Gct | Tct | 2 | 3 | P.1.17 | 0.000324 |
S | 222 | A222S | GcT | TcA | 1 | 3 | P.1.17 | 0.000162 |
S | 222 | A222S | Gct | Tct | 2 | 2 | AD.2 | 0.000438 |
S | 222 | A222S | Gct | Tct | 2 | 2 | AY.105 | 0.001286 |
S | 222 | A222S | Gct | Tct | 2 | 2 | AY.36 | 0.000296 |
S | 222 | A222S | Gct | Tct | 2 | 2 | AY.4.2 | 0.000043 |
S | 222 | A222S | Gct | Tct | 2 | 2 | AY.5.3 | 0.000675 |
S | 222 | A222S | Gct | Tct | 2 | 2 | AY.7.1 | 0.000225 |
S | 222 | A222S | Gct | Tct | 2 | 2 | B.1.1.25 | 0.001137 |
S | 222 | A222S | Gct | Tct | 2 | 2 | B.1.160 | 0.000062 |
S | 222 | A222S | Gct | Tct | 2 | 2 | B.1.243 | 0.000139 |
S | 222 | A222S | Gct | Tct | 2 | 2 | B.1.351 | 0.000059 |
S | 222 | A222S | Gct | Tct | 2 | 2 | B.1.36 | 0.000292 |
S | 222 | A222S | Gct | Tct | 2 | 2 | B.1.470 | 0.002809 |
S | 222 | A222S | Gct | Tct | 2 | 2 | B.1.596 | 0.000174 |
S | 222 | A222S | Gct | Tct | 2 | 2 | D.2 | 0.00015 |
S | 222 | A222S | Gct | Tct | 1 | 1 | A | 0.000387 |
S | 222 | A222S | Gct | Tct | 1 | 1 | A.2.5 | 0.000499 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.114 | 0.000231 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.14 | 0.000088 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.15 | 0.002222 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.16.1 | 0.00047 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.29.1 | 0.000221 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.39.1 | 0.00004 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.39.1.1 | 0.000725 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.4.4 | 0.000409 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.45 | 0.000122 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.47 | 0.000031 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.5.4 | 0.000277 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.64 | 0.000595 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.83 | 0.001724 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.84 | 0.000437 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.92 | 0.000287 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.93 | 0.000273 |
S | 222 | A222S | Gct | Tct | 1 | 1 | AY.99 | 0.001049 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1 | 0.000018 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.142 | 0.017544 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.159 | 0.004673 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.176 | 0.000439 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.214 | 0.000055 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.239 | 0.032258 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.241 | 0.00207 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.304 | 0.002809 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.317 | 0.000412 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.318 | 0.000302 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.348 | 0.000796 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.372 | 0.000689 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.434 | 0.000349 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.50 | 0.000679 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.1.63 | 0.000386 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.240 | 0.000216 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.369 | 0.000285 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.416 | 0.001269 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.517 | 0.000427 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.617.1 | 0.000129 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.617.3 | 0.002985 |
S | 222 | A222S | Gct | Tct | 1 | 1 | B.1.634 | 0.003425 |
S | 222 | A222S | Gct | Tct | 1 | 1 | P.1.15 | 0.000232 |
S | 222 | A222S | Gct | Tct | 1 | 1 | P.2 | 0.000187 |
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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