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 |
ORF7a | 40 | Y40H | nonsyn | Tac | Cac | 1062 | 1058 | 0.996234 | 27511-27513 | |
ORF7a | 40 | Y40H | nonsyn | TaC | CaT | 1062 | 4 | 0.00376648 | 27511-27513 |
Details of the mutation Y40H 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 |
ORF7a | 40 | Y40H | Tac | Cac | 1058 | 1062 | All | 0.000202 |
ORF7a | 40 | Y40H | TaC | CaT | 4 | 1062 | All | 0.000001 |
ORF7a | 40 | Y40H | Tac | Cac | 334 | 334 | B.1.1.7 | 0.000299 |
ORF7a | 40 | Y40H | Tac | Cac | 287 | 287 | AY.4 | 0.000447 |
ORF7a | 40 | Y40H | Tac | Cac | 46 | 46 | AY.43 | 0.000204 |
ORF7a | 40 | Y40H | Tac | Cac | 35 | 35 | AY.103 | 0.000217 |
ORF7a | 40 | Y40H | Tac | Cac | 33 | 33 | B.1.637 | 0.002411 |
ORF7a | 40 | Y40H | Tac | Cac | 26 | 26 | B.1.617.2 | 0.000098 |
ORF7a | 40 | Y40H | Tac | Cac | 24 | 24 | AY.25 | 0.000144 |
ORF7a | 40 | Y40H | Tac | Cac | 22 | 22 | P.1 | 0.000347 |
ORF7a | 40 | Y40H | Tac | Cac | 19 | 19 | B.1 | 0.000174 |
ORF7a | 40 | Y40H | Tac | Cac | 18 | 18 | AY.27 | 0.001165 |
ORF7a | 40 | Y40H | Tac | Cac | 14 | 14 | AY.106 | 0.004689 |
ORF7a | 40 | Y40H | Tac | Cac | 12 | 13 | AY.3 | 0.000119 |
ORF7a | 40 | Y40H | TaC | CaT | 1 | 13 | AY.3 | 0.00001 |
ORF7a | 40 | Y40H | Tac | Cac | 13 | 13 | AY.44 | 0.000079 |
ORF7a | 40 | Y40H | Tac | Cac | 10 | 10 | P.1.7 | 0.003193 |
ORF7a | 40 | Y40H | Tac | Cac | 9 | 9 | AY.111 | 0.001648 |
ORF7a | 40 | Y40H | Tac | Cac | 9 | 9 | AY.26 | 0.000255 |
ORF7a | 40 | Y40H | Tac | Cac | 8 | 8 | AY.39 | 0.000198 |
ORF7a | 40 | Y40H | Tac | Cac | 7 | 7 | B.1.621 | 0.00062 |
ORF7a | 40 | Y40H | Tac | Cac | 6 | 6 | AY.3.1 | 0.000512 |
ORF7a | 40 | Y40H | Tac | Cac | 6 | 6 | B.1.2 | 0.000053 |
ORF7a | 40 | Y40H | Tac | Cac | 5 | 5 | AY.109 | 0.003698 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 4 | 0.111111 | |
ORF7a | 40 | Y40H | TaC | CaT | 2 | 4 | 0.111111 | |
ORF7a | 40 | Y40H | Tac | Cac | 4 | 4 | AY.100 | 0.000184 |
ORF7a | 40 | Y40H | Tac | Cac | 4 | 4 | AY.4.2 | 0.000087 |
ORF7a | 40 | Y40H | Tac | Cac | 4 | 4 | AY.54 | 0.000381 |
ORF7a | 40 | Y40H | Tac | Cac | 4 | 4 | B.1.1.176 | 0.001757 |
ORF7a | 40 | Y40H | Tac | Cac | 4 | 4 | B.1.128 | 0.002541 |
ORF7a | 40 | Y40H | Tac | Cac | 4 | 4 | B.1.160 | 0.000125 |
ORF7a | 40 | Y40H | Tac | Cac | 4 | 4 | P.1.10 | 0.001078 |
ORF7a | 40 | Y40H | Tac | Cac | 3 | 3 | AY.102 | 0.00008 |
ORF7a | 40 | Y40H | Tac | Cac | 3 | 3 | AY.14 | 0.000264 |
ORF7a | 40 | Y40H | Tac | Cac | 3 | 3 | AY.46.6 | 0.000217 |
ORF7a | 40 | Y40H | Tac | Cac | 3 | 3 | B.1.1 | 0.000054 |
ORF7a | 40 | Y40H | Tac | Cac | 3 | 3 | B.1.1.519 | 0.000119 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AY.114 | 0.000462 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AY.117 | 0.000169 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AY.119 | 0.000071 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AY.13 | 0.000322 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AY.23 | 0.000139 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AY.47 | 0.000062 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AY.49 | 0.00639 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | AZ.2 | 0.001642 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.1.210 | 0.011429 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.1.222 | 0.000408 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.1.372 | 0.001377 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.243 | 0.000139 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.36.10 | 0.009569 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.429 | 0.000047 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.596 | 0.000174 |
ORF7a | 40 | Y40H | Tac | Cac | 2 | 2 | B.1.617.1 | 0.000258 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AM.4 | 0.003571 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.116 | 0.000287 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.20 | 0.000039 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.29 | 0.000016 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.39.1 | 0.00004 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.45 | 0.000122 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.46.4 | 0.000165 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.46.5 | 0.000198 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.66 | 0.00107 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.77 | 0.001127 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.82 | 0.001357 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.9 | 0.000068 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.9.2 | 0.000037 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.93 | 0.000273 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.98.1 | 0.000048 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | AY.99.2 | 0.000092 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.1.348 | 0.000796 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.177 | 0.000013 |
ORF7a | 40 | Y40H | TaC | CaT | 1 | 1 | B.1.177.63 | 0.002703 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.177.7 | 0.000165 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.221 | 0.000071 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.258.17 | 0.000104 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.351 | 0.00003 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.36.16 | 0.001425 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.36.8 | 0.001 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.416.1 | 0.001563 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.468 | 0.005714 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.525 | 0.000113 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.526 | 0.000024 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.564 | 0.000426 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.628 | 0.000352 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | B.1.88.1 | 0.004808 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | C.1.2 | 0.004255 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | D.2 | 0.000075 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | P.1.14 | 0.000048 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | P.1.15 | 0.000232 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | Q.8 | 0.000165 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | R.1 | 0.00009 |
ORF7a | 40 | Y40H | Tac | Cac | 1 | 1 | S.1 | 0.00495 |
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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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