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 | 1306 | T1306T | T2124T | syn | acT | acC | 1626 | 1334 | 0.820418 | 6635-6637 |
ORF1ab/nsp3 | 1306 | T1306T | T2124T | syn | acT | acA | 1626 | 160 | 0.098401 | 6635-6637 |
ORF1ab/nsp3 | 1306 | T1306T | T2124T | syn | acT | acG | 1626 | 132 | 0.0811808 | 6635-6637 |
Details of the mutation T1306T 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 | 1306 | T1306T | acT | acC | 1334 | 1626 | All | 0.000255 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 160 | 1626 | All | 0.000031 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 132 | 1626 | All | 0.000025 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1133 | 1160 | B.1.1.7 | 0.001014 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 24 | 1160 | B.1.1.7 | 0.000021 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 3 | 1160 | B.1.1.7 | 0.000003 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 83 | 171 | AY.4 | 0.000129 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 71 | 171 | AY.4 | 0.000111 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 17 | 171 | AY.4 | 0.000026 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 50 | 51 | AY.4.2 | 0.001084 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 51 | AY.4.2 | 0.000022 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 32 | 32 | R.1 | 0.00288 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 26 | 26 | AY.44 | 0.000158 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 14 | 19 | B.1.617.2 | 0.000053 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 3 | 19 | B.1.617.2 | 0.000011 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 2 | 19 | B.1.617.2 | 0.000008 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 7 | 14 | AY.3 | 0.00007 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 6 | 14 | AY.3 | 0.00006 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 14 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 14 | 14 | P.1.15 | 0.003253 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 10 | 12 | AY.6 | 0.000411 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 12 | AY.6 | 0.000082 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 6 | 10 | AY.103 | 0.000037 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 4 | 10 | AY.103 | 0.000025 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 6 | 8 | B.1 | 0.000055 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 2 | 8 | B.1 | 0.000018 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 7 | 7 | B.1.258 | 0.000466 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 7 | 7 | P.2 | 0.001306 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 6 | 6 | B.1.1.381 | 0.24 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 4 | 6 | B.1.1.519 | 0.000159 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 2 | 6 | B.1.1.519 | 0.000079 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 5 | 5 | B.1.369 | 0.001426 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 2 | 4 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 4 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 4 | 4 | AY.9.1 | 0.000335 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 3 | 3 | 0.166667 | |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 2 | 3 | AY.23 | 0.000139 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 3 | AY.23 | 0.00007 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 3 | 3 | AY.32 | 0.001597 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 3 | AY.43 | 0.000009 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 3 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 3 | 3 | B.1.1.63 | 0.001157 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 2 | A.5 | 0.003846 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 2 | AY.111 | 0.000366 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 2 | AY.30 | 0.000791 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 2 | 2 | AY.45 | 0.000243 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 2 | B | 0.000128 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 2 | B | 0.000128 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 2 | B.1.1.306 | 0.000877 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 2 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 2 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 2 | 2 | B.1.177.81 | 0.000379 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | AY.23.1 | 0.000417 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | AY.37 | 0.000316 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | AY.46.1 | 0.001027 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | AY.69 | 0.000187 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | AY.89 | 0.004902 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | B.1.1.220 | 0.001859 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.1.298 | 0.000862 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.1.432 | 0.001266 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.1.464 | 0.001473 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.177.15 | 0.000631 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.177.33 | 0.001645 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.177.42 | 0.000894 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acA | 1 | 1 | B.1.177.54 | 0.000606 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | B.1.221.2 | 0.004016 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.298 | 0.002114 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.433 | 0.003195 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.438.1 | 0.000107 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acG | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp3 | 1306 | T1306T | acT | acC | 1 | 1 | P.1 | 0.000016 |
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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