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 | 617 | I617I | I1435I | syn | atC | atT | 2239 | 2108 | 0.941492 | 4568-4570 |
ORF1ab/nsp3 | 617 | I617I | I1435I | syn | atC | atA | 2239 | 131 | 0.0585083 | 4568-4570 |
Details of the mutation I617I 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 | 617 | I617I | atC | atT | 2108 | 2239 | All | 0.000403 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 131 | 2239 | All | 0.000025 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1189 | 1229 | B.1.1.7 | 0.001064 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 40 | 1229 | B.1.1.7 | 0.000036 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 77 | 78 | AY.25 | 0.000463 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 78 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 73 | 75 | AY.43 | 0.000323 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 2 | 75 | AY.43 | 0.000009 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 59 | 63 | B.1.617.2 | 0.000222 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 4 | 63 | B.1.617.2 | 0.000015 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 53 | 53 | AY.44 | 0.000323 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 53 | 53 | B.1.348 | 0.963636 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 45 | 46 | AY.4 | 0.00007 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 46 | AY.4 | 0.000002 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 45 | 45 | B.1.258 | 0.002995 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 42 | 42 | AY.46 | 0.004371 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 42 | 42 | B.1.2 | 0.00037 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 35 | 35 | AY.79 | 0.042373 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 30 | 31 | AY.5 | 0.000619 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 31 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 25 | 28 | B.1.621 | 0.002213 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 28 | B.1.621 | 0.000266 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 26 | 27 | AY.26 | 0.000736 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 27 | AY.26 | 0.000028 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 27 | 27 | P.1 | 0.000425 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 21 | 26 | B.1 | 0.000192 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 5 | 26 | B.1 | 0.000046 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 26 | 26 | B.1.1 | 0.000472 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 25 | 25 | AY.9.2 | 0.000918 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 20 | 20 | AY.99.2 | 0.001843 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 19 | 19 | B.1.221 | 0.00135 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 18 | 18 | B.1.177.44 | 0.009341 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 17 | 17 | AY.24 | 0.007328 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 13 | 13 | B.1.526 | 0.000306 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 10 | 10 | B.1.160 | 0.000312 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 8 | 8 | AY.47 | 0.000249 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 7 | 7 | AY.39 | 0.000173 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 6 | 6 | AY.103 | 0.000037 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 6 | 6 | AY.119 | 0.000212 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 6 | 6 | AY.46.2 | 0.003812 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 4 | 5 | AY.3 | 0.00004 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 5 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 5 | 5 | B.1.177.21 | 0.000382 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 4 | AY.102 | 0.00008 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 4 | AY.102 | 0.000027 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 4 | 4 | AY.20 | 0.000155 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 4 | 4 | AY.23 | 0.000279 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 4 | 4 | B.1.416 | 0.005076 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 4 | C.37 | 0.000348 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 4 | C.37 | 0.000116 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | A.2.5 | 0.001497 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 2 | 3 | AY.113 | 0.000285 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 3 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 3 | AY.118 | 0.000125 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 3 | AY.118 | 0.000063 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | AY.85 | 0.001282 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.1.214 | 0.000166 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.1.385 | 0.013393 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.1.440 | 0.035294 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.1.519 | 0.000119 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.1.526 | 0.010638 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.177 | 0.00004 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.234 | 0.000396 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 3 | 3 | B.1.369 | 0.000856 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 3 | B.1.429 | 0.000047 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 3 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.114 | 0.000462 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.14 | 0.000176 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.29 | 0.000032 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.4.5 | 0.000215 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 2 | AY.52 | 0.000814 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 2 | AY.52 | 0.000814 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.54 | 0.000191 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.7.1 | 0.000225 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | AY.75.1 | 0.000361 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 2 | 2 | B.1.1.306 | 0.000877 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | B.1.1.486 | 0.003155 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | B.1.126 | 0.002551 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | B.1.177.5 | 0.002484 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | B.1.222 | 0.003384 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | B.1.582 | 0.000981 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 2 | 2 | P.1.14 | 0.000096 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | A | 0.000387 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AT.1 | 0.005128 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.107 | 0.000466 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.120.2 | 0.001285 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.29.1 | 0.000221 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.5.3 | 0.000337 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | AY.87 | 0.000833 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B | 0.000128 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.1.170 | 0.001247 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.1.263 | 0.001558 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 1 | B.1.1.275 | 0.011236 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.1.294 | 0.001266 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.1.416 | 0.000905 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.177.42 | 0.000894 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.177.62 | 0.001192 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.337 | 0.005587 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 1 | B.1.36.22 | 0.001208 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.36.31 | 0.001751 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp3 | 617 | I617I | atC | atA | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.524 | 0.001406 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.568 | 0.001111 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.576 | 0.000907 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.605 | 0.005952 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.625 | 0.002353 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | B.1.93 | 0.000934 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | N.3 | 0.005814 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | Q.8 | 0.000165 |
ORF1ab/nsp3 | 617 | I617I | atC | atT | 1 | 1 | Z.1 | 0.00289 |
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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