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 |
ORF3a | 143 | A143A | syn | gcC | gcT | 1570 | 1476 | 0.940127 | 25819-25821 | |
ORF3a | 143 | A143A | syn | gcC | gcA | 1570 | 78 | 0.0496815 | 25819-25821 | |
ORF3a | 143 | A143A | syn | gcC | gcG | 1570 | 16 | 0.0101911 | 25819-25821 |
Details of the mutation A143A 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 |
ORF3a | 143 | A143A | gcC | gcT | 1476 | 1570 | All | 0.000282 |
ORF3a | 143 | A143A | gcC | gcA | 78 | 1570 | All | 0.000015 |
ORF3a | 143 | A143A | gcC | gcG | 16 | 1570 | All | 0.000003 |
ORF3a | 143 | A143A | gcC | gcT | 756 | 757 | AY.44 | 0.004602 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 757 | AY.44 | 0.000006 |
ORF3a | 143 | A143A | gcC | gcT | 129 | 139 | B.1.1.7 | 0.000115 |
ORF3a | 143 | A143A | gcC | gcA | 10 | 139 | B.1.1.7 | 0.000009 |
ORF3a | 143 | A143A | gcC | gcT | 129 | 137 | AY.4 | 0.000201 |
ORF3a | 143 | A143A | gcC | gcA | 6 | 137 | AY.4 | 0.000009 |
ORF3a | 143 | A143A | gcC | gcG | 2 | 137 | AY.4 | 0.000003 |
ORF3a | 143 | A143A | gcC | gcT | 111 | 113 | B.1 | 0.001017 |
ORF3a | 143 | A143A | gcC | gcG | 1 | 113 | B.1 | 0.000009 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 113 | B.1 | 0.000009 |
ORF3a | 143 | A143A | gcC | gcT | 100 | 100 | AY.25 | 0.000601 |
ORF3a | 143 | A143A | gcC | gcT | 38 | 46 | B.1.617.2 | 0.000143 |
ORF3a | 143 | A143A | gcC | gcA | 8 | 46 | B.1.617.2 | 0.00003 |
ORF3a | 143 | A143A | gcC | gcT | 27 | 28 | P.1 | 0.000425 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 28 | P.1 | 0.000016 |
ORF3a | 143 | A143A | gcC | gcT | 19 | 19 | B.1.324 | 0.030498 |
ORF3a | 143 | A143A | gcC | gcA | 17 | 18 | AY.5 | 0.000351 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 18 | AY.5 | 0.000021 |
ORF3a | 143 | A143A | gcC | gcT | 11 | 11 | A.2.5.2 | 0.017296 |
ORF3a | 143 | A143A | gcC | gcA | 10 | 11 | AY.3 | 0.000099 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 11 | AY.3 | 0.00001 |
ORF3a | 143 | A143A | gcC | gcT | 11 | 11 | B.1.36.38 | 0.018062 |
ORF3a | 143 | A143A | gcC | gcT | 10 | 10 | AY.26 | 0.000283 |
ORF3a | 143 | A143A | gcC | gcT | 10 | 10 | B.1.2 | 0.000088 |
ORF3a | 143 | A143A | gcC | gcT | 8 | 9 | AY.43 | 0.000035 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 9 | AY.43 | 0.000004 |
ORF3a | 143 | A143A | gcC | gcA | 4 | 8 | B.1.1 | 0.000073 |
ORF3a | 143 | A143A | gcC | gcT | 4 | 8 | B.1.1 | 0.000073 |
ORF3a | 143 | A143A | gcC | gcG | 8 | 8 | B.1.1.50 | 0.005431 |
ORF3a | 143 | A143A | gcC | gcT | 6 | 7 | B.1.351 | 0.000178 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 7 | B.1.351 | 0.00003 |
ORF3a | 143 | A143A | gcC | gcT | 7 | 7 | P.1.15 | 0.001626 |
ORF3a | 143 | A143A | gcC | gcT | 6 | 6 | AY.100 | 0.000276 |
ORF3a | 143 | A143A | gcC | gcT | 4 | 5 | AY.103 | 0.000025 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 5 | AY.103 | 0.000006 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 4 | AY.117 | 0.000169 |
ORF3a | 143 | A143A | gcC | gcA | 2 | 4 | AY.117 | 0.000169 |
ORF3a | 143 | A143A | gcC | gcA | 2 | 4 | AY.119 | 0.000071 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 4 | AY.119 | 0.000071 |
ORF3a | 143 | A143A | gcC | gcT | 3 | 4 | AY.39 | 0.000074 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 4 | AY.39 | 0.000025 |
ORF3a | 143 | A143A | gcC | gcT | 4 | 4 | B.1.466.2 | 0.001565 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 4 | B.1.526 | 0.000047 |
ORF3a | 143 | A143A | gcC | gcA | 2 | 4 | B.1.526 | 0.000047 |
ORF3a | 143 | A143A | gcC | gcT | 4 | 4 | B.1.623 | 0.002146 |
ORF3a | 143 | A143A | gcC | gcT | 3 | 3 | AY.29 | 0.000047 |
ORF3a | 143 | A143A | gcC | gcA | 2 | 3 | AY.98.1 | 0.000097 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 3 | AY.98.1 | 0.000048 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 3 | B | 0.000128 |
ORF3a | 143 | A143A | gcC | gcG | 1 | 3 | B | 0.000128 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 3 | B | 0.000128 |
ORF3a | 143 | A143A | gcC | gcT | 3 | 3 | B.1.177.12 | 0.000455 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 3 | B.1.427 | 0.000101 |
ORF3a | 143 | A143A | gcC | gcG | 1 | 3 | B.1.427 | 0.00005 |
ORF3a | 143 | A143A | gcC | gcT | 3 | 3 | B.1.621 | 0.000266 |
ORF3a | 143 | A143A | gcC | gcT | 3 | 3 | B.1.637 | 0.000219 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | AY.120.2.1 | 0.000997 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | AY.13 | 0.000322 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | AY.20 | 0.000078 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | AY.47 | 0.000062 |
ORF3a | 143 | A143A | gcC | gcA | 2 | 2 | AY.9 | 0.000135 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | AY.92 | 0.000575 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | B.1.1.28 | 0.000622 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | B.1.1.420 | 0.002012 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | B.1.1.519 | 0.000079 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | B.1.177 | 0.000026 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | B.1.177.44 | 0.001038 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | B.1.177.54 | 0.001213 |
ORF3a | 143 | A143A | gcC | gcT | 2 | 2 | P.1.14 | 0.000096 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | A | 0.000387 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AW.1 | 0.003049 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AY.102 | 0.000027 |
ORF3a | 143 | A143A | gcC | gcG | 1 | 1 | AY.37 | 0.000316 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AY.39.1 | 0.00004 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 1 | AY.4.2 | 0.000022 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 1 | AY.46.2 | 0.000635 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AY.6 | 0.000041 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AY.61 | 0.000105 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 1 | AY.7.1 | 0.000113 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 1 | AY.75 | 0.000056 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AY.75.1 | 0.00018 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AY.98 | 0.000079 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | AY.99.2 | 0.000092 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.1.157 | 0.000913 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.1.214 | 0.000055 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.1.348 | 0.000796 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.1.419 | 0.007407 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.140 | 0.018868 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.177.11 | 0.001698 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.177.75 | 0.001041 |
ORF3a | 143 | A143A | gcC | gcG | 1 | 1 | B.1.223 | 0.002778 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.241 | 0.000812 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.243 | 0.00007 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.280 | 0.007143 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.36.29 | 0.000517 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.400 | 0.000429 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.429 | 0.000024 |
ORF3a | 143 | A143A | gcC | gcG | 1 | 1 | B.1.450 | 0.011364 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.556 | 0.007519 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.596 | 0.000087 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.609 | 0.000479 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | B.1.8 | 0.001972 |
ORF3a | 143 | A143A | gcC | gcA | 1 | 1 | B.6 | 0.00091 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | C.36.3 | 0.000567 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | D.2 | 0.000075 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | P.1.10 | 0.000269 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | Q.1 | 0.000126 |
ORF3a | 143 | A143A | gcC | gcT | 1 | 1 | Q.3 | 0.000145 |
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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