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 |
M | 31 | W31C | nonsyn | tgG | tgT | 311 | 301 | 0.967846 | 26613-26615 | |
M | 31 | W31C | nonsyn | tgG | tgC | 311 | 10 | 0.0321543 | 26613-26615 | |
M | 31 | W31L | nonsyn | tGg | tTg | 109 | 109 | 1 | 26613-26615 | |
M | 31 | W31del | del | TGG | --- | 31 | 31 | 1 | 26613-26615 | |
M | 31 | W31X | nonsyn | tgG | tgA | 8 | 5 | 0.625 | 26613-26615 | |
M | 31 | W31G | nonsyn | Tgg | Ggg | 8 | 5 | 0.625 | 26613-26615 | |
M | 31 | W31X | nonsyn | tGg | tAg | 8 | 3 | 0.375 | 26613-26615 | |
M | 31 | W31G | nonsyn | TgG | GgT | 8 | 2 | 0.25 | 26613-26615 | |
M | 31 | W31G | nonsyn | TgG | GgA | 8 | 1 | 0.125 | 26613-26615 | |
M | 31 | W31R | nonsyn | Tgg | Cgg | 7 | 6 | 0.857143 | 26613-26615 | |
M | 31 | W31R | nonsyn | Tgg | Agg | 7 | 1 | 0.142857 | 26613-26615 | |
M | 31 | W31S | nonsyn | tGg | tCg | 4 | 3 | 0.75 | 26613-26615 | |
M | 31 | W31S | nonsyn | tGG | tCA | 4 | 1 | 0.25 | 26613-26615 | |
M | 31 | W31del1 | del | Tgg | -gg | 3 | 2 | 0.666667 | 26613-26615 | |
M | 31 | W31del1 | del | tGg | t-g | 3 | 1 | 0.333333 | 26613-26615 | |
M | 31 | W31F | nonsyn | tGG | tTT | 2 | 2 | 1 | 26613-26615 | |
M | 31 | W31Y | nonsyn | tGG | tAC | 1 | 1 | 1 | 26613-26615 | |
M | 31 | W31A | nonsyn | TGG | GCA | 1 | 1 | 1 | 26613-26615 | |
M | 31 | W31Q | nonsyn | TGG | CAA | 1 | 1 | 1 | 26613-26615 | |
M | 31 | W31V | nonsyn | TGG | GTT | 1 | 1 | 1 | 26613-26615 |
Details of the mutation no 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 |
M | 31 | W31C | tgG | tgT | 301 | 311 | All | 0.000058 |
M | 31 | W31C | tgG | tgC | 10 | 311 | All | 0.000002 |
M | 31 | W31L | tGg | tTg | 109 | 109 | All | 0.000021 |
M | 31 | W31C | tgG | tgT | 67 | 67 | B.1.1.43 | 1 |
M | 31 | W31C | tgG | tgT | 61 | 62 | B.1.1.7 | 0.000055 |
M | 31 | W31C | tgG | tgC | 1 | 62 | B.1.1.7 | 0.000001 |
M | 31 | W31del | TGG | --- | 31 | 31 | All | 0.000006 |
M | 31 | W31C | tgG | tgT | 29 | 29 | AY.4 | 0.000045 |
M | 31 | W31L | tGg | tTg | 19 | 19 | B.1.617.2 | 0.000072 |
M | 31 | W31L | tGg | tTg | 11 | 11 | B.1.1.519 | 0.000437 |
M | 31 | W31L | tGg | tTg | 10 | 10 | AY.23 | 0.000697 |
M | 31 | W31C | tgG | tgT | 9 | 9 | AY.100 | 0.000414 |
M | 31 | W31C | tgG | tgT | 9 | 9 | B.1 | 0.000082 |
M | 31 | W31L | tGg | tTg | 9 | 9 | B.1.1.7 | 0.000008 |
M | 31 | W31C | tgG | tgT | 9 | 9 | B.1.160 | 0.000281 |
M | 31 | W31L | tGg | tTg | 9 | 9 | B.1.637 | 0.000658 |
M | 31 | W31X | tgG | tgA | 5 | 8 | All | 0.000001 |
M | 31 | W31G | Tgg | Ggg | 5 | 8 | All | 0.000001 |
M | 31 | W31X | tGg | tAg | 3 | 8 | All | 0.000001 |
M | 31 | W31G | TgG | GgT | 2 | 8 | All | 0 |
M | 31 | W31G | TgG | GgA | 1 | 8 | All | 0 |
M | 31 | W31C | tgG | tgT | 8 | 8 | AY.103 | 0.00005 |
M | 31 | W31del | TGG | --- | 8 | 8 | B.1.177.21 | 0.000612 |
M | 31 | W31C | tgG | tgT | 8 | 8 | B.1.240 | 0.001725 |
M | 31 | W31C | tgG | tgT | 8 | 8 | B.1.617.2 | 0.00003 |
M | 31 | W31R | Tgg | Cgg | 6 | 7 | All | 0.000001 |
M | 31 | W31R | Tgg | Agg | 1 | 7 | All | 0 |
M | 31 | W31C | tgG | tgT | 7 | 7 | AY.25 | 0.000042 |
M | 31 | W31del | TGG | --- | 7 | 7 | B.1.1.7 | 0.000006 |
M | 31 | W31C | tgG | tgT | 7 | 7 | B.1.258.17 | 0.000728 |
M | 31 | W31C | tgG | tgT | 5 | 5 | AY.20 | 0.000194 |
M | 31 | W31C | tgG | tgT | 5 | 5 | B.1.1 | 0.000091 |
M | 31 | W31C | tgG | tgT | 5 | 5 | P.1 | 0.000079 |
M | 31 | W31del | TGG | --- | 4 | 4 | 0.222222 | |
M | 31 | W31S | tGg | tCg | 3 | 4 | All | 0.000001 |
M | 31 | W31S | tGG | tCA | 1 | 4 | All | 0 |
M | 31 | W31C | tgG | tgT | 3 | 4 | AY.102 | 0.00008 |
M | 31 | W31C | tgG | tgC | 1 | 4 | AY.102 | 0.000027 |
M | 31 | W31L | tGg | tTg | 4 | 4 | AY.103 | 0.000025 |
M | 31 | W31C | tgG | tgT | 3 | 4 | AY.43 | 0.000013 |
M | 31 | W31C | tgG | tgC | 1 | 4 | AY.43 | 0.000004 |
M | 31 | W31L | tGg | tTg | 4 | 4 | AY.5 | 0.000083 |
M | 31 | W31C | tgG | tgT | 4 | 4 | B.1.110.3 | 0.002874 |
M | 31 | W31C | tgG | tgT | 4 | 4 | B.1.2 | 0.000035 |
M | 31 | W31del1 | Tgg | -gg | 2 | 3 | All | 0 |
M | 31 | W31del1 | tGg | t-g | 1 | 3 | All | 0 |
M | 31 | W31C | tgG | tgT | 3 | 3 | AY.119 | 0.000106 |
M | 31 | W31L | tGg | tTg | 3 | 3 | AY.25 | 0.000018 |
M | 31 | W31C | tgG | tgT | 3 | 3 | AY.44 | 0.000018 |
M | 31 | W31C | tgG | tgC | 3 | 3 | AY.93 | 0.000819 |
M | 31 | W31L | tGg | tTg | 3 | 3 | B.1 | 0.000027 |
M | 31 | W31X | tgG | tgA | 2 | 3 | B.1 | 0.000018 |
M | 31 | W31X | tGg | tAg | 1 | 3 | B.1 | 0.000009 |
M | 31 | W31L | tGg | tTg | 3 | 3 | B.1.1 | 0.000054 |
M | 31 | W31C | tgG | tgT | 3 | 3 | B.1.177 | 0.00004 |
M | 31 | W31L | tGg | tTg | 3 | 3 | B.1.177.86 | 0.00055 |
M | 31 | W31L | tGg | tTg | 3 | 3 | P.1 | 0.000047 |
M | 31 | W31C | tgG | tgT | 3 | 3 | P.1.14 | 0.000143 |
M | 31 | W31G | TgG | GgT | 2 | 2 | 0.111111 | |
M | 31 | W31F | tGG | tTT | 2 | 2 | All | 0 |
M | 31 | W31L | tGg | tTg | 2 | 2 | AY.118 | 0.000125 |
M | 31 | W31L | tGg | tTg | 2 | 2 | AY.34 | 0.000194 |
M | 31 | W31C | tgG | tgT | 2 | 2 | AY.39 | 0.000049 |
M | 31 | W31L | tGg | tTg | 2 | 2 | AY.43 | 0.000009 |
M | 31 | W31C | tgG | tgT | 2 | 2 | AY.47 | 0.000062 |
M | 31 | W31C | tgG | tgT | 2 | 2 | AY.5.2 | 0.004926 |
M | 31 | W31del | TGG | --- | 2 | 2 | B.1 | 0.000018 |
M | 31 | W31C | tgG | tgT | 2 | 2 | B.1.1.214 | 0.000111 |
M | 31 | W31C | tgG | tgT | 2 | 2 | B.1.1.99 | 0.047619 |
M | 31 | W31L | tGg | tTg | 2 | 2 | B.1.160 | 0.000062 |
M | 31 | W31L | tGg | tTg | 2 | 2 | B.1.2 | 0.000018 |
M | 31 | W31C | tgG | tgT | 2 | 2 | B.1.526 | 0.000047 |
M | 31 | W31C | tgG | tgT | 2 | 2 | B.1.619 | 0.001742 |
M | 31 | W31del1 | Tgg | -gg | 2 | 2 | B.1.627 | 0.00404 |
M | 31 | W31del | TGG | --- | 2 | 2 | P.1 | 0.000032 |
M | 31 | W31C | tgG | tgT | 1 | 1 | 0.055556 | |
M | 31 | W31L | tGg | tTg | 1 | 1 | 0.055556 | |
M | 31 | W31F | tGG | tTT | 1 | 1 | 0.055556 | |
M | 31 | W31A | TGG | GCA | 1 | 1 | All | 0 |
M | 31 | W31Y | tGG | tAC | 1 | 1 | All | 0 |
M | 31 | W31V | TGG | GTT | 1 | 1 | All | 0 |
M | 31 | W31Q | TGG | CAA | 1 | 1 | All | 0 |
M | 31 | W31A | TGG | GCA | 1 | 1 | AY.117 | 0.000085 |
M | 31 | W31del | TGG | --- | 1 | 1 | AY.120 | 0.000037 |
M | 31 | W31L | tGg | tTg | 1 | 1 | AY.120 | 0.000037 |
M | 31 | W31F | tGG | tTT | 1 | 1 | AY.26 | 0.000028 |
M | 31 | W31C | tgG | tgT | 1 | 1 | AY.29.1 | 0.000221 |
M | 31 | W31S | tGg | tCg | 1 | 1 | AY.3 | 0.00001 |
M | 31 | W31C | tgG | tgT | 1 | 1 | AY.3 | 0.00001 |
M | 31 | W31C | tgG | tgT | 1 | 1 | AY.34.1 | 0.00051 |
M | 31 | W31C | tgG | tgC | 1 | 1 | AY.39.1 | 0.00004 |
M | 31 | W31del | TGG | --- | 1 | 1 | AY.4 | 0.000002 |
M | 31 | W31L | tGg | tTg | 1 | 1 | AY.4 | 0.000002 |
M | 31 | W31G | Tgg | Ggg | 1 | 1 | AY.4 | 0.000002 |
M | 31 | W31C | tgG | tgT | 1 | 1 | AY.4.2 | 0.000022 |
M | 31 | W31del | TGG | --- | 1 | 1 | AY.4.5 | 0.000107 |
M | 31 | W31L | tGg | tTg | 1 | 1 | AY.4.5 | 0.000107 |
M | 31 | W31R | Tgg | Cgg | 1 | 1 | AY.43 | 0.000004 |
M | 31 | W31L | tGg | tTg | 1 | 1 | AY.44 | 0.000006 |
M | 31 | W31del1 | tGg | t-g | 1 | 1 | AY.44 | 0.000006 |
M | 31 | W31C | tgG | tgT | 1 | 1 | AY.46.6 | 0.000072 |
M | 31 | W31L | tGg | tTg | 1 | 1 | AY.46.6 | 0.000072 |
M | 31 | W31L | tGg | tTg | 1 | 1 | AY.6 | 0.000041 |
M | 31 | W31del | TGG | --- | 1 | 1 | AY.68 | 0.000274 |
M | 31 | W31C | tgG | tgT | 1 | 1 | AY.74 | 0.000116 |
M | 31 | W31C | tgG | tgT | 1 | 1 | AY.9.2 | 0.000037 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B | 0.000128 |
M | 31 | W31S | tGg | tCg | 1 | 1 | B.1 | 0.000009 |
M | 31 | W31G | Tgg | Ggg | 1 | 1 | B.1 | 0.000009 |
M | 31 | W31G | TgG | GgA | 1 | 1 | B.1.1 | 0.000018 |
M | 31 | W31R | Tgg | Cgg | 1 | 1 | B.1.1 | 0.000018 |
M | 31 | W31X | tgG | tgA | 1 | 1 | B.1.1 | 0.000018 |
M | 31 | W31S | tGG | tCA | 1 | 1 | B.1.1.153 | 0.001095 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.1.284 | 0.000107 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.1.318 | 0.000302 |
M | 31 | W31Q | TGG | CAA | 1 | 1 | B.1.1.372 | 0.000689 |
M | 31 | W31C | tgG | tgC | 1 | 1 | B.1.1.398 | 0.003226 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.1.420 | 0.001006 |
M | 31 | W31Y | tGG | tAC | 1 | 1 | B.1.1.7 | 0.000001 |
M | 31 | W31G | Tgg | Ggg | 1 | 1 | B.1.1.7 | 0.000001 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.157 | 0.002985 |
M | 31 | W31S | tGg | tCg | 1 | 1 | B.1.160.12 | 0.00641 |
M | 31 | W31del | TGG | --- | 1 | 1 | B.1.161 | 0.017241 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.177.5 | 0.001242 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.177.56 | 0.000668 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.177.73 | 0.000566 |
M | 31 | W31G | Tgg | Ggg | 1 | 1 | B.1.177.8 | 0.000752 |
M | 31 | W31C | tgG | tgC | 1 | 1 | B.1.177.9 | 0.001332 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.215 | 0.009615 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.234 | 0.000132 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.243 | 0.00007 |
M | 31 | W31C | tgG | tgC | 1 | 1 | B.1.258 | 0.000067 |
M | 31 | W31R | Tgg | Agg | 1 | 1 | B.1.351 | 0.00003 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.36 | 0.000146 |
M | 31 | W31X | tgG | tgA | 1 | 1 | B.1.36.7 | 0.004 |
M | 31 | W31X | tgG | tgA | 1 | 1 | B.1.396 | 0.000706 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.400 | 0.000429 |
M | 31 | W31G | Tgg | Ggg | 1 | 1 | B.1.422 | 0.000812 |
M | 31 | W31R | Tgg | Cgg | 1 | 1 | B.1.427 | 0.00005 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.427 | 0.00005 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.429 | 0.000024 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.429 | 0.000024 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.438.1 | 0.000107 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.456 | 0.003268 |
M | 31 | W31X | tGg | tAg | 1 | 1 | B.1.466.2 | 0.000391 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.517.1 | 0.005263 |
M | 31 | W31X | tGg | tAg | 1 | 1 | B.1.554 | 0.004405 |
M | 31 | W31del | TGG | --- | 1 | 1 | B.1.577 | 0.000687 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.595 | 0.000261 |
M | 31 | W31R | Tgg | Cgg | 1 | 1 | B.1.596 | 0.000087 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.609 | 0.000479 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.1.617.1 | 0.000129 |
M | 31 | W31R | Tgg | Cgg | 1 | 1 | B.1.617.2 | 0.000004 |
M | 31 | W31C | tgG | tgT | 1 | 1 | B.1.621 | 0.000089 |
M | 31 | W31del | TGG | --- | 1 | 1 | B.1.627 | 0.00202 |
M | 31 | W31V | TGG | GTT | 1 | 1 | B.1.630 | 0.005236 |
M | 31 | W31L | tGg | tTg | 1 | 1 | B.29 | 0.003509 |
M | 31 | W31C | tgG | tgT | 1 | 1 | D.2 | 0.000075 |
M | 31 | W31R | Tgg | Cgg | 1 | 1 | P.1 | 0.000016 |
M | 31 | W31del | TGG | --- | 1 | 1 | P.1.15 | 0.000232 |
M | 31 | W31C | tgG | tgT | 1 | 1 | P.1.15 | 0.000232 |
M | 31 | W31L | tGg | tTg | 1 | 1 | W.2 | 0.004831 |
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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