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 |
ORF3a | 23 | A23A | syn | gcT | gcC | 1968 | 1713 | 0.870427 | 25459-25461 | |
ORF3a | 23 | A23A | syn | gcT | gcA | 1968 | 233 | 0.118394 | 25459-25461 | |
ORF3a | 23 | A23A | syn | gcT | gcG | 1968 | 22 | 0.0111789 | 25459-25461 |
Details of the mutation A23A 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 |
ORF3a | 23 | A23A | gcT | gcC | 1713 | 1968 | All | 0.000328 |
ORF3a | 23 | A23A | gcT | gcA | 233 | 1968 | All | 0.000045 |
ORF3a | 23 | A23A | gcT | gcG | 22 | 1968 | All | 0.000004 |
ORF3a | 23 | A23A | gcT | gcC | 335 | 340 | B.1.1.7 | 0.0003 |
ORF3a | 23 | A23A | gcT | gcA | 5 | 340 | B.1.1.7 | 0.000004 |
ORF3a | 23 | A23A | gcT | gcC | 252 | 255 | AY.44 | 0.001534 |
ORF3a | 23 | A23A | gcT | gcA | 3 | 255 | AY.44 | 0.000018 |
ORF3a | 23 | A23A | gcT | gcC | 210 | 231 | AY.4 | 0.000327 |
ORF3a | 23 | A23A | gcT | gcG | 21 | 231 | AY.4 | 0.000033 |
ORF3a | 23 | A23A | gcT | gcA | 114 | 227 | B.1.617.2 | 0.000429 |
ORF3a | 23 | A23A | gcT | gcC | 113 | 227 | B.1.617.2 | 0.000425 |
ORF3a | 23 | A23A | gcT | gcC | 163 | 165 | AY.20 | 0.006335 |
ORF3a | 23 | A23A | gcT | gcA | 2 | 165 | AY.20 | 0.000078 |
ORF3a | 23 | A23A | gcT | gcC | 149 | 149 | B.1.2 | 0.001312 |
ORF3a | 23 | A23A | gcT | gcA | 56 | 60 | AY.102 | 0.001485 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 60 | AY.102 | 0.000106 |
ORF3a | 23 | A23A | gcT | gcC | 48 | 48 | AY.25 | 0.000289 |
ORF3a | 23 | A23A | gcT | gcC | 45 | 45 | AU.2 | 0.108959 |
ORF3a | 23 | A23A | gcT | gcC | 34 | 35 | AY.120 | 0.001264 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 35 | AY.120 | 0.000037 |
ORF3a | 23 | A23A | gcT | gcC | 28 | 29 | AY.103 | 0.000174 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 29 | AY.103 | 0.000006 |
ORF3a | 23 | A23A | gcT | gcC | 25 | 29 | AY.39 | 0.000618 |
ORF3a | 23 | A23A | gcT | gcA | 4 | 29 | AY.39 | 0.000099 |
ORF3a | 23 | A23A | gcT | gcC | 29 | 29 | AY.5 | 0.000599 |
ORF3a | 23 | A23A | gcT | gcC | 9 | 18 | AY.43 | 0.00004 |
ORF3a | 23 | A23A | gcT | gcA | 9 | 18 | AY.43 | 0.00004 |
ORF3a | 23 | A23A | gcT | gcC | 17 | 17 | B.1.177 | 0.000224 |
ORF3a | 23 | A23A | gcT | gcC | 13 | 15 | AY.117 | 0.001099 |
ORF3a | 23 | A23A | gcT | gcA | 2 | 15 | AY.117 | 0.000169 |
ORF3a | 23 | A23A | gcT | gcC | 15 | 15 | AY.30 | 0.005936 |
ORF3a | 23 | A23A | gcT | gcC | 13 | 13 | C.38 | 0.104839 |
ORF3a | 23 | A23A | gcT | gcC | 13 | 13 | P.1 | 0.000205 |
ORF3a | 23 | A23A | gcT | gcC | 12 | 12 | B.1.351 | 0.000357 |
ORF3a | 23 | A23A | gcT | gcC | 7 | 10 | AY.3 | 0.00007 |
ORF3a | 23 | A23A | gcT | gcA | 3 | 10 | AY.3 | 0.00003 |
ORF3a | 23 | A23A | gcT | gcC | 10 | 10 | AY.4.2 | 0.000217 |
ORF3a | 23 | A23A | gcT | gcA | 10 | 10 | B.1.243 | 0.000696 |
ORF3a | 23 | A23A | gcT | gcC | 10 | 10 | B.1.429 | 0.000235 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 7 | AY.3.1 | 0.000341 |
ORF3a | 23 | A23A | gcT | gcA | 3 | 7 | AY.3.1 | 0.000256 |
ORF3a | 23 | A23A | gcT | gcC | 7 | 7 | AY.78 | 0.010786 |
ORF3a | 23 | A23A | gcT | gcC | 7 | 7 | B.1.621 | 0.00062 |
ORF3a | 23 | A23A | gcT | gcC | 7 | 7 | B.1.637 | 0.000512 |
ORF3a | 23 | A23A | gcT | gcC | 5 | 5 | AY.29 | 0.000079 |
ORF3a | 23 | A23A | gcT | gcC | 5 | 5 | AY.61 | 0.000524 |
ORF3a | 23 | A23A | gcT | gcC | 3 | 5 | B.1.1 | 0.000054 |
ORF3a | 23 | A23A | gcT | gcA | 2 | 5 | B.1.1 | 0.000036 |
ORF3a | 23 | A23A | gcT | gcC | 5 | 5 | B.4 | 0.011038 |
ORF3a | 23 | A23A | gcT | gcC | 5 | 5 | Q.7 | 0.005556 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 4 | AY.100 | 0.000184 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 4 | AY.108 | 0.00441 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 4 | AY.4.4 | 0.001637 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 4 | AY.45 | 0.000487 |
ORF3a | 23 | A23A | gcT | gcA | 3 | 4 | AY.46 | 0.000312 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 4 | AY.46 | 0.000104 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 4 | AY.97 | 0.006803 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 4 | B.1.258 | 0.000266 |
ORF3a | 23 | A23A | gcT | gcC | 4 | 4 | R.1 | 0.00036 |
ORF3a | 23 | A23A | gcT | gcC | 3 | 3 | AY.119 | 0.000106 |
ORF3a | 23 | A23A | gcT | gcC | 3 | 3 | AY.32 | 0.001597 |
ORF3a | 23 | A23A | gcT | gcA | 3 | 3 | AY.4.2.1 | 0.000447 |
ORF3a | 23 | A23A | gcT | gcC | 3 | 3 | AY.92 | 0.000862 |
ORF3a | 23 | A23A | gcT | gcC | 3 | 3 | AY.99.2 | 0.000276 |
ORF3a | 23 | A23A | gcT | gcC | 3 | 3 | B.1 | 0.000027 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 3 | B.1.1.222 | 0.000408 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 3 | B.1.1.222 | 0.000204 |
ORF3a | 23 | A23A | gcT | gcC | 3 | 3 | C.36 | 0.002732 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.105 | 0.001286 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.116 | 0.000574 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.13 | 0.000322 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.23 | 0.000139 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.26 | 0.000057 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.4.5 | 0.000215 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.46.3 | 0.001867 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 2 | AY.46.6 | 0.000072 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 2 | AY.46.6 | 0.000072 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | AY.81 | 0.003984 |
ORF3a | 23 | A23A | gcT | gcA | 2 | 2 | AY.9.2 | 0.000073 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | B.1.1.28 | 0.000622 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | B.1.240 | 0.000431 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | B.1.313 | 0.013158 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | B.1.427 | 0.000101 |
ORF3a | 23 | A23A | gcT | gcC | 2 | 2 | B.1.617.1 | 0.000258 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | A.2.5.2 | 0.001572 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AD.2 | 0.000219 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.1 | 0.000396 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.113 | 0.000142 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.16 | 0.00038 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.16.1 | 0.00047 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | AY.34 | 0.000097 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.38 | 0.000499 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | AY.39.1 | 0.00004 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.47 | 0.000031 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.54 | 0.000095 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.55 | 0.000917 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.65 | 0.000533 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.70 | 0.000209 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.75 | 0.000056 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | AY.86 | 0.00083 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.9 | 0.000068 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.95 | 0.000761 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | AY.98 | 0.000079 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B | 0.000128 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.1.10 | 0.001115 |
ORF3a | 23 | A23A | gcT | gcG | 1 | 1 | B.1.1.194 | 0.00495 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.1.214 | 0.000055 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.1.237 | 0.005405 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.1.31 | 0.066667 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | B.1.1.318 | 0.000302 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | B.1.160 | 0.000031 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.177.8 | 0.000752 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.177.81 | 0.000189 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.221 | 0.000071 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.258.17 | 0.000104 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | B.1.351.2 | 0.000303 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | B.1.369 | 0.000285 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.404 | 0.001302 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.524 | 0.001406 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.525 | 0.000113 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.543 | 0.01 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.596 | 0.000087 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.1.625 | 0.002353 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | B.4.7 | 0.010101 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | C.36.3 | 0.000567 |
ORF3a | 23 | A23A | gcT | gcA | 1 | 1 | P.1.14 | 0.000048 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | P.1.15 | 0.000232 |
ORF3a | 23 | A23A | gcT | gcC | 1 | 1 | P.1.7 | 0.000319 |
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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