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 |
ORF1ab/nsp3 | 667 | A667A | A1485A | syn | gcG | gcA | 4831 | 1055 | 0.218381 | 4718-4720 |
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 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1055 | 4831 | All | 0.000202 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 53 | 612 | B.1.1.7 | 0.000047 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 444 | 608 | AY.4 | 0.000691 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 44 | 337 | B.1.617.2 | 0.000166 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 16 | 197 | AY.103 | 0.000099 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 76 | 141 | AY.25 | 0.000457 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 36 | 132 | AY.43 | 0.000159 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 6 | 131 | B.1.160 | 0.000187 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 19 | 118 | AY.44 | 0.000116 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 59 | 107 | B.1.2 | 0.00052 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 3 | 104 | AY.102 | 0.00008 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 24 | 97 | AY.3 | 0.000239 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 10 | 92 | AY.4.5 | 0.001075 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 7 | 81 | AY.20 | 0.000272 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 17 | 52 | B.1 | 0.000156 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 49 | P.1 | 0.000032 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 41 | AY.99.2 | 0.000092 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 8 | 34 | AY.33 | 0.000534 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 10 | 31 | AY.39 | 0.000247 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 27 | B.1.1 | 0.000036 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 27 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 8 | 23 | AY.47 | 0.000249 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 21 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 4 | 20 | AY.23 | 0.000279 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 19 | 19 | AY.95 | 0.01446 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 16 | 18 | B.1.1.28 | 0.00498 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 18 | 18 | B.1.470 | 0.025281 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 17 | 17 | B.1.1.171 | 0.0625 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 10 | 15 | AY.61 | 0.001048 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 14 | AY.118 | 0.000063 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 4 | 14 | AY.26 | 0.000113 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 14 | AY.29 | 0.000016 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 7 | 14 | AY.5 | 0.000145 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 5 | 13 | B.1.258 | 0.000333 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 13 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 12 | AY.100 | 0.000046 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 9 | 12 | AY.46.4 | 0.001481 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 12 | B.1.36 | 0.000146 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 3 | 12 | B.1.526 | 0.000071 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 4 | 11 | AY.98.1 | 0.000194 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 6 | 8 | A | 0.002322 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 5 | 8 | B.1.1.214 | 0.000277 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 3 | 7 | B.1.243 | 0.000209 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 6 | AY.9.2 | 0.000073 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 6 | B.1.1.37 | 0.000193 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 5 | AY.39.1 | 0.00004 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 5 | 5 | B.1.221.2 | 0.02008 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 3 | 5 | B.1.311 | 0.000824 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 5 | 5 | B.1.324 | 0.008026 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 4 | AY.46 | 0.000104 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 4 | AY.68 | 0.000274 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 4 | 4 | AY.84 | 0.00175 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 4 | B.1.1.50 | 0.000679 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 4 | 4 | B.1.1.63 | 0.001543 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 3 | 3 | A.2.5 | 0.001497 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 3 | 3 | AY.105 | 0.001929 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 3 | 3 | AY.120 | 0.000112 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 3 | AY.55 | 0.001835 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 3 | P.1.14 | 0.000048 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 2 | 0.111111 | |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 2 | AY.34.1 | 0.00051 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 2 | AY.36 | 0.000148 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 2 | AY.5.3 | 0.000337 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 2 | AY.65 | 0.000533 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 2 | AY.79 | 0.002421 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 2 | AY.85 | 0.000427 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 2 | B.1.1.277 | 0.000759 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 2 | B.1.160.28 | 0.005848 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 2 | 2 | B.1.561 | 0.000794 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | AY.4.3 | 0.000842 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | AY.51 | 0.000909 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.1.253 | 0.002506 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.1.333 | 0.001076 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.177.19 | 0.001431 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.241 | 0.000812 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.258.21 | 0.007752 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.36.17 | 0.000494 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.426 | 0.001009 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.428.2 | 0.033333 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.518 | 0.011765 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.575 | 0.000303 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.585 | 0.027778 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp3 | 667 | A667A | gcG | gcA | 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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