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 | 143 | V143V | syn | gtT | gtG | 595 | 365 | 0.613445 | 21989-21991 | |
S | 143 | V143V | syn | gtT | gtC | 595 | 128 | 0.215126 | 21989-21991 | |
S | 143 | V143V | syn | gtT | gtA | 595 | 102 | 0.171429 | 21989-21991 |
Details of the mutation V143V 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 | 143 | V143V | gtT | gtG | 365 | 595 | All | 0.00007 |
S | 143 | V143V | gtT | gtC | 128 | 595 | All | 0.000024 |
S | 143 | V143V | gtT | gtA | 102 | 595 | All | 0.00002 |
S | 143 | V143V | gtT | gtC | 83 | 109 | B.1.1.7 | 0.000074 |
S | 143 | V143V | gtT | gtG | 23 | 109 | B.1.1.7 | 0.000021 |
S | 143 | V143V | gtT | gtA | 3 | 109 | B.1.1.7 | 0.000003 |
S | 143 | V143V | gtT | gtA | 71 | 73 | B.1.621 | 0.006285 |
S | 143 | V143V | gtT | gtC | 2 | 73 | B.1.621 | 0.000177 |
S | 143 | V143V | gtT | gtG | 55 | 55 | AY.44 | 0.000335 |
S | 143 | V143V | gtT | gtG | 30 | 31 | AY.103 | 0.000186 |
S | 143 | V143V | gtT | gtC | 1 | 31 | AY.103 | 0.000006 |
S | 143 | V143V | gtT | gtG | 31 | 31 | B.1 | 0.000284 |
S | 143 | V143V | gtT | gtG | 19 | 27 | B.1.617.2 | 0.000072 |
S | 143 | V143V | gtT | gtC | 7 | 27 | B.1.617.2 | 0.000026 |
S | 143 | V143V | gtT | gtA | 1 | 27 | B.1.617.2 | 0.000004 |
S | 143 | V143V | gtT | gtA | 18 | 19 | B.1.621.1 | 0.009105 |
S | 143 | V143V | gtT | gtC | 1 | 19 | B.1.621.1 | 0.000506 |
S | 143 | V143V | gtT | gtG | 15 | 16 | B.1.617.1 | 0.001934 |
S | 143 | V143V | gtT | gtC | 1 | 16 | B.1.617.1 | 0.000129 |
S | 143 | V143V | gtT | gtG | 14 | 15 | AY.39 | 0.000346 |
S | 143 | V143V | gtT | gtC | 1 | 15 | AY.39 | 0.000025 |
S | 143 | V143V | gtT | gtG | 15 | 15 | B.1.1 | 0.000272 |
S | 143 | V143V | gtT | gtG | 13 | 14 | AY.25 | 0.000078 |
S | 143 | V143V | gtT | gtA | 1 | 14 | AY.25 | 0.000006 |
S | 143 | V143V | gtT | gtG | 12 | 13 | AY.3 | 0.000119 |
S | 143 | V143V | gtT | gtC | 1 | 13 | AY.3 | 0.00001 |
S | 143 | V143V | gtT | gtC | 12 | 13 | AY.3.1 | 0.001023 |
S | 143 | V143V | gtT | gtG | 1 | 13 | AY.3.1 | 0.000085 |
S | 143 | V143V | gtT | gtG | 11 | 12 | AY.69 | 0.002053 |
S | 143 | V143V | gtT | gtC | 1 | 12 | AY.69 | 0.000187 |
S | 143 | V143V | gtT | gtG | 12 | 12 | B | 0.001534 |
S | 143 | V143V | gtT | gtG | 9 | 11 | AY.117 | 0.000761 |
S | 143 | V143V | gtT | gtC | 2 | 11 | AY.117 | 0.000169 |
S | 143 | V143V | gtT | gtG | 7 | 8 | AY.43 | 0.000031 |
S | 143 | V143V | gtT | gtC | 1 | 8 | AY.43 | 0.000004 |
S | 143 | V143V | gtT | gtG | 5 | 6 | AY.23 | 0.000349 |
S | 143 | V143V | gtT | gtA | 1 | 6 | AY.23 | 0.00007 |
S | 143 | V143V | gtT | gtG | 6 | 6 | AY.26 | 0.00017 |
S | 143 | V143V | gtT | gtG | 5 | 6 | AY.4 | 0.000008 |
S | 143 | V143V | gtT | gtA | 1 | 6 | AY.4 | 0.000002 |
S | 143 | V143V | gtT | gtG | 4 | 5 | B.1.429 | 0.000094 |
S | 143 | V143V | gtT | gtC | 1 | 5 | B.1.429 | 0.000024 |
S | 143 | V143V | gtT | gtG | 4 | 4 | AY.20 | 0.000155 |
S | 143 | V143V | gtT | gtG | 4 | 4 | AY.47 | 0.000124 |
S | 143 | V143V | gtT | gtG | 4 | 4 | AY.54 | 0.000381 |
S | 143 | V143V | gtT | gtG | 3 | 4 | AY.75 | 0.000168 |
S | 143 | V143V | gtT | gtA | 1 | 4 | AY.75 | 0.000056 |
S | 143 | V143V | gtT | gtG | 3 | 3 | AY.113 | 0.000427 |
S | 143 | V143V | gtT | gtG | 3 | 3 | AY.120.1 | 0.000963 |
S | 143 | V143V | gtT | gtA | 2 | 3 | AY.96 | 0.004149 |
S | 143 | V143V | gtT | gtG | 1 | 3 | AY.96 | 0.002075 |
S | 143 | V143V | gtT | gtG | 3 | 3 | B.1.1.220 | 0.005576 |
S | 143 | V143V | gtT | gtG | 3 | 3 | B.1.36.10 | 0.014354 |
S | 143 | V143V | gtT | gtC | 1 | 2 | AY.100 | 0.000046 |
S | 143 | V143V | gtT | gtG | 1 | 2 | AY.100 | 0.000046 |
S | 143 | V143V | gtT | gtG | 2 | 2 | AY.114 | 0.000462 |
S | 143 | V143V | gtT | gtG | 2 | 2 | AY.119 | 0.000071 |
S | 143 | V143V | gtT | gtG | 1 | 2 | AY.24 | 0.000431 |
S | 143 | V143V | gtT | gtC | 1 | 2 | AY.24 | 0.000431 |
S | 143 | V143V | gtT | gtC | 1 | 2 | AY.5 | 0.000021 |
S | 143 | V143V | gtT | gtA | 1 | 2 | AY.5 | 0.000021 |
S | 143 | V143V | gtT | gtG | 2 | 2 | AY.5.3 | 0.000675 |
S | 143 | V143V | gtT | gtG | 2 | 2 | AY.61 | 0.00021 |
S | 143 | V143V | gtT | gtG | 2 | 2 | AY.81 | 0.003984 |
S | 143 | V143V | gtT | gtG | 1 | 2 | B.1.1.409 | 0.002833 |
S | 143 | V143V | gtT | gtC | 1 | 2 | B.1.1.409 | 0.002833 |
S | 143 | V143V | gtT | gtG | 2 | 2 | B.1.36 | 0.000292 |
S | 143 | V143V | gtT | gtG | 2 | 2 | B.1.36.29 | 0.001035 |
S | 143 | V143V | gtT | gtC | 1 | 1 | 0.055556 | |
S | 143 | V143V | gtT | gtG | 1 | 1 | A.29 | 0.005319 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AU.2 | 0.002421 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.120.2 | 0.001285 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.121 | 0.000135 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.14 | 0.000088 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.16 | 0.00038 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.33 | 0.000067 |
S | 143 | V143V | gtT | gtC | 1 | 1 | AY.38 | 0.000499 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.4.5 | 0.000107 |
S | 143 | V143V | gtT | gtC | 1 | 1 | AY.42 | 0.00004 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.46 | 0.000104 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.48 | 0.000465 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.59 | 0.00053 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.65 | 0.000533 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.71 | 0.000475 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.77 | 0.001127 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.84 | 0.000437 |
S | 143 | V143V | gtT | gtG | 1 | 1 | AY.88 | 0.000884 |
S | 143 | V143V | gtT | gtA | 1 | 1 | AY.9 | 0.000068 |
S | 143 | V143V | gtT | gtA | 1 | 1 | AY.94 | 0.000443 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.1.306 | 0.000438 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.1.318 | 0.000302 |
S | 143 | V143V | gtT | gtC | 1 | 1 | B.1.1.420 | 0.001006 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.1.507 | 0.008696 |
S | 143 | V143V | gtT | gtC | 1 | 1 | B.1.160 | 0.000031 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.170 | 0.00431 |
S | 143 | V143V | gtT | gtC | 1 | 1 | B.1.177.7 | 0.000165 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.177.73 | 0.000566 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.2 | 0.000009 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.221 | 0.000071 |
S | 143 | V143V | gtT | gtC | 1 | 1 | B.1.351 | 0.00003 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.36.8 | 0.001 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.427 | 0.00005 |
S | 143 | V143V | gtT | gtC | 1 | 1 | B.1.466 | 0.023256 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.470 | 0.001404 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.538 | 0.008065 |
S | 143 | V143V | gtT | gtC | 1 | 1 | B.1.582 | 0.000491 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.595 | 0.000261 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.617.3 | 0.002985 |
S | 143 | V143V | gtT | gtG | 1 | 1 | B.1.630 | 0.005236 |
S | 143 | V143V | gtT | gtC | 1 | 1 | B.1.637 | 0.000073 |
S | 143 | V143V | gtT | gtG | 1 | 1 | P.1 | 0.000016 |
S | 143 | V143V | gtT | gtG | 1 | 1 | Q.1 | 0.000126 |
S | 143 | V143V | gtT | gtG | 1 | 1 | S.1 | 0.00495 |
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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