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 | 244 | L244L | syn | Tta | Cta | 695 | 524 | 0.753957 | 22292-22294 | |
S | 244 | L244L | syn | ttA | ttG | 695 | 166 | 0.238849 | 22292-22294 | |
S | 244 | L244L | syn | TtA | CtT | 695 | 4 | 0.0057554 | 22292-22294 | |
S | 244 | L244L | syn | TtA | CtC | 695 | 1 | 0.00143885 | 22292-22294 |
Details of the mutation L244L 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 | 244 | L244L | Tta | Cta | 524 | 695 | All | 0.0001 |
S | 244 | L244L | ttA | ttG | 166 | 695 | All | 0.000032 |
S | 244 | L244L | TtA | CtT | 4 | 695 | All | 0.000001 |
S | 244 | L244L | TtA | CtC | 1 | 695 | All | 0 |
S | 244 | L244L | Tta | Cta | 141 | 183 | AY.4 | 0.000219 |
S | 244 | L244L | ttA | ttG | 42 | 183 | AY.4 | 0.000065 |
S | 244 | L244L | Tta | Cta | 175 | 176 | AY.102 | 0.00464 |
S | 244 | L244L | TtA | CtT | 1 | 176 | AY.102 | 0.000027 |
S | 244 | L244L | Tta | Cta | 57 | 71 | B.1.617.2 | 0.000215 |
S | 244 | L244L | ttA | ttG | 14 | 71 | B.1.617.2 | 0.000053 |
S | 244 | L244L | ttA | ttG | 14 | 26 | B.1.1.7 | 0.000013 |
S | 244 | L244L | Tta | Cta | 12 | 26 | B.1.1.7 | 0.000011 |
S | 244 | L244L | Tta | Cta | 15 | 23 | B.1.2 | 0.000132 |
S | 244 | L244L | ttA | ttG | 8 | 23 | B.1.2 | 0.00007 |
S | 244 | L244L | Tta | Cta | 13 | 16 | AY.43 | 0.000058 |
S | 244 | L244L | ttA | ttG | 3 | 16 | AY.43 | 0.000013 |
S | 244 | L244L | ttA | ttG | 16 | 16 | AY.75 | 0.000896 |
S | 244 | L244L | ttA | ttG | 16 | 16 | Q.4 | 0.007276 |
S | 244 | L244L | ttA | ttG | 14 | 14 | B.1.265 | 0.017789 |
S | 244 | L244L | Tta | Cta | 11 | 12 | AY.44 | 0.000067 |
S | 244 | L244L | ttA | ttG | 1 | 12 | AY.44 | 0.000006 |
S | 244 | L244L | Tta | Cta | 10 | 11 | B.1.177 | 0.000132 |
S | 244 | L244L | TtA | CtT | 1 | 11 | B.1.177 | 0.000013 |
S | 244 | L244L | ttA | ttG | 4 | 8 | AY.103 | 0.000025 |
S | 244 | L244L | Tta | Cta | 4 | 8 | AY.103 | 0.000025 |
S | 244 | L244L | Tta | Cta | 6 | 7 | AY.118 | 0.000376 |
S | 244 | L244L | ttA | ttG | 1 | 7 | AY.118 | 0.000063 |
S | 244 | L244L | Tta | Cta | 5 | 7 | B.1 | 0.000046 |
S | 244 | L244L | ttA | ttG | 2 | 7 | B.1 | 0.000018 |
S | 244 | L244L | Tta | Cta | 7 | 7 | P.1 | 0.00011 |
S | 244 | L244L | Tta | Cta | 6 | 6 | B.1.429 | 0.000141 |
S | 244 | L244L | Tta | Cta | 3 | 5 | AY.4.5 | 0.000322 |
S | 244 | L244L | ttA | ttG | 2 | 5 | AY.4.5 | 0.000215 |
S | 244 | L244L | Tta | Cta | 4 | 4 | AY.98.1 | 0.000194 |
S | 244 | L244L | ttA | ttG | 3 | 3 | AY.20 | 0.000117 |
S | 244 | L244L | Tta | Cta | 3 | 3 | AY.26 | 0.000085 |
S | 244 | L244L | Tta | Cta | 3 | 3 | AY.34.1 | 0.00153 |
S | 244 | L244L | Tta | Cta | 3 | 3 | AY.46 | 0.000312 |
S | 244 | L244L | Tta | Cta | 3 | 3 | AY.46.1 | 0.00308 |
S | 244 | L244L | ttA | ttG | 3 | 3 | AY.61 | 0.000314 |
S | 244 | L244L | Tta | Cta | 3 | 3 | AY.98 | 0.000237 |
S | 244 | L244L | Tta | Cta | 3 | 3 | B.1.1.311 | 0.001074 |
S | 244 | L244L | Tta | Cta | 3 | 3 | B.1.177.82 | 0.001432 |
S | 244 | L244L | ttA | ttG | 3 | 3 | B.1.214.2 | 0.001799 |
S | 244 | L244L | Tta | Cta | 2 | 2 | AY.1 | 0.000791 |
S | 244 | L244L | Tta | Cta | 2 | 2 | AY.119 | 0.000071 |
S | 244 | L244L | ttA | ttG | 2 | 2 | AY.14 | 0.000176 |
S | 244 | L244L | Tta | Cta | 2 | 2 | AY.39 | 0.000049 |
S | 244 | L244L | Tta | Cta | 1 | 2 | AY.4.2 | 0.000022 |
S | 244 | L244L | ttA | ttG | 1 | 2 | AY.4.2 | 0.000022 |
S | 244 | L244L | Tta | Cta | 2 | 2 | AY.5 | 0.000041 |
S | 244 | L244L | ttA | ttG | 2 | 2 | AY.53 | 0.000575 |
S | 244 | L244L | ttA | ttG | 1 | 2 | B.1.1 | 0.000018 |
S | 244 | L244L | Tta | Cta | 1 | 2 | B.1.1 | 0.000018 |
S | 244 | L244L | ttA | ttG | 1 | 2 | B.1.1.519 | 0.00004 |
S | 244 | L244L | Tta | Cta | 1 | 2 | B.1.1.519 | 0.00004 |
S | 244 | L244L | ttA | ttG | 2 | 2 | B.1.36 | 0.000292 |
S | 244 | L244L | Tta | Cta | 2 | 2 | B.1.517 | 0.000854 |
S | 244 | L244L | ttA | ttG | 2 | 2 | B.1.621 | 0.000177 |
S | 244 | L244L | Tta | Cta | 1 | 1 | A.3 | 0.002096 |
S | 244 | L244L | ttA | ttG | 1 | 1 | AY.101 | 0.00049 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.113 | 0.000142 |
S | 244 | L244L | ttA | ttG | 1 | 1 | AY.120 | 0.000037 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.23 | 0.00007 |
S | 244 | L244L | ttA | ttG | 1 | 1 | AY.25 | 0.000006 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.29.1 | 0.000221 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.3 | 0.00001 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.36 | 0.000148 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.42 | 0.00004 |
S | 244 | L244L | ttA | ttG | 1 | 1 | AY.55 | 0.000917 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.84 | 0.000437 |
S | 244 | L244L | Tta | Cta | 1 | 1 | AY.9 | 0.000068 |
S | 244 | L244L | TtA | CtT | 1 | 1 | B.1.1.1 | 0.000327 |
S | 244 | L244L | ttA | ttG | 1 | 1 | B.1.1.189 | 0.001513 |
S | 244 | L244L | ttA | ttG | 1 | 1 | B.1.1.204 | 0.00304 |
S | 244 | L244L | ttA | ttG | 1 | 1 | B.1.1.214 | 0.000055 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.177.4 | 0.000211 |
S | 244 | L244L | ttA | ttG | 1 | 1 | B.1.221 | 0.000071 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.240 | 0.000216 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.258 | 0.000067 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.258.17 | 0.000104 |
S | 244 | L244L | TtA | CtC | 1 | 1 | B.1.351.1 | 0.038462 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.36.19 | 0.009259 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.526 | 0.000024 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.577 | 0.000687 |
S | 244 | L244L | Tta | Cta | 1 | 1 | B.1.639 | 0.021739 |
S | 244 | L244L | ttA | ttG | 1 | 1 | B.6.6 | 0.000889 |
S | 244 | L244L | Tta | Cta | 1 | 1 | C.37 | 0.000116 |
S | 244 | L244L | Tta | Cta | 1 | 1 | D.2 | 0.000075 |
S | 244 | L244L | Tta | Cta | 1 | 1 | P.1.12 | 0.000484 |
S | 244 | L244L | TtA | CtT | 1 | 1 | P.3 | 0.001595 |
S | 244 | L244L | Tta | Cta | 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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