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/nsp13 | 199 | T199T | T5523T | syn | acC | acT | 914 | 780 | 0.853392 | 16831-16833 |
ORF1ab/nsp13 | 199 | T199T | T5523T | syn | acC | acA | 914 | 133 | 0.145514 | 16831-16833 |
ORF1ab/nsp13 | 199 | T199T | T5523T | syn | acC | acG | 914 | 1 | 0.00109409 | 16831-16833 |
Details of the mutation T199T 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/nsp13 | 199 | T199T | acC | acT | 780 | 914 | All | 0.000149 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 133 | 914 | All | 0.000025 |
ORF1ab/nsp13 | 199 | T199T | acC | acG | 1 | 914 | All | 0 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 372 | 372 | B.1.258.22 | 0.992 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 117 | 145 | B.1.1.7 | 0.000105 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 28 | 145 | B.1.1.7 | 0.000025 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 40 | 40 | B.1.2 | 0.000352 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 35 | 35 | B.1.1.398 | 0.112903 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 21 | 34 | B.1.617.2 | 0.000079 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 13 | 34 | B.1.617.2 | 0.000049 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 29 | 30 | AY.25 | 0.000174 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 30 | AY.25 | 0.000006 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 28 | 29 | AY.43 | 0.000124 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 29 | AY.43 | 0.000004 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 24 | 24 | B.1.160.19 | 0.857143 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 17 | 19 | AY.3 | 0.000169 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 19 | AY.3 | 0.00002 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 9 | 14 | AY.4 | 0.000014 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 5 | 14 | AY.4 | 0.000008 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 7 | 13 | AY.44 | 0.000043 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 6 | 13 | AY.44 | 0.000037 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 9 | 13 | B.1 | 0.000082 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 4 | 13 | B.1 | 0.000037 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 13 | 13 | B.1.177 | 0.000171 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 8 | 10 | B.1.1 | 0.000145 |
ORF1ab/nsp13 | 199 | T199T | acC | acG | 1 | 10 | B.1.1 | 0.000018 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 10 | B.1.1 | 0.000018 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 9 | 9 | B.1.427 | 0.000454 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 8 | 8 | B.1.1.333 | 0.008611 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 8 | 8 | B.1.525 | 0.000905 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 6 | 7 | AY.39 | 0.000148 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 7 | AY.39 | 0.000025 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 7 | 7 | P.1.15 | 0.001626 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 4 | 6 | AY.103 | 0.000025 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 2 | 6 | AY.103 | 0.000012 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 6 | 6 | AY.70 | 0.001251 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 5 | 5 | AY.110 | 0.000563 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 3 | AY.23 | 0.000139 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 3 | AY.23 | 0.00007 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 3 | 3 | AY.29 | 0.000047 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 3 | 3 | AY.75.1 | 0.000541 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 3 | 3 | B.1.596 | 0.000261 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 3 | P.1 | 0.000032 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 3 | P.1 | 0.000016 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 2 | AY.100 | 0.000092 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 2 | AY.102 | 0.000027 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 2 | AY.102 | 0.000027 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 2 | 2 | AY.71 | 0.00095 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 2 | B.1.1.335 | 0.025974 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 2 | 2 | B.1.637 | 0.000146 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 2 | B.1.93 | 0.001867 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 2 | 2 | P.2 | 0.000373 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | A.2 | 0.000662 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | A.23.1 | 0.000704 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | AY.37 | 0.000316 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | AY.7 | 0.000196 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | B.1.1.523 | 0.001563 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.351.2 | 0.000303 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | B.1.36.31 | 0.001751 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.396 | 0.000706 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.408 | 0.00369 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.409 | 0.000781 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.564 | 0.000426 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.1.636 | 0.006711 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | B.3 | 0.000831 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp13 | 199 | T199T | acC | acA | 1 | 1 | P.1.7 | 0.000319 |
ORF1ab/nsp13 | 199 | T199T | acC | acT | 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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