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 | 140 | A140A | A5464A | syn | gcT | gcC | 612 | 574 | 0.937908 | 16654-16656 |
ORF1ab/nsp13 | 140 | A140A | A5464A | syn | gcT | gcA | 612 | 30 | 0.0490196 | 16654-16656 |
ORF1ab/nsp13 | 140 | A140A | A5464A | syn | gcT | gcG | 612 | 8 | 0.0130719 | 16654-16656 |
Details of the mutation A140A 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 | 140 | A140A | gcT | gcC | 574 | 612 | All | 0.00011 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 30 | 612 | All | 0.000006 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcG | 8 | 612 | All | 0.000002 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 261 | 264 | B.1.1.7 | 0.000234 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 3 | 264 | B.1.1.7 | 0.000003 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 52 | 52 | B.1.438.2 | 1 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 31 | 31 | B.1.577 | 0.021306 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 30 | 30 | B.1.525 | 0.003395 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 27 | 28 | AY.4 | 0.000042 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcG | 1 | 28 | AY.4 | 0.000002 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 28 | 28 | AY.43 | 0.000124 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 17 | 19 | B.1.617.2 | 0.000064 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcG | 1 | 19 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 1 | 19 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 17 | 18 | AY.119 | 0.0006 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 18 | AY.119 | 0.000035 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 15 | 15 | B.1.1 | 0.000272 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 7 | 7 | B.1.2 | 0.000062 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 3 | 6 | B.1 | 0.000027 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 3 | 6 | B.1 | 0.000027 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 5 | 5 | AY.102 | 0.000133 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 5 | 5 | AY.103 | 0.000031 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 5 | 5 | B.1.160 | 0.000156 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 4 | 4 | AY.25 | 0.000024 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 4 | 4 | AY.26 | 0.000113 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 4 | 4 | AY.39.1 | 0.000158 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 4 | 4 | AY.4.2 | 0.000087 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcG | 4 | 4 | B.1.177 | 0.000053 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 4 | 4 | B.1.351 | 0.000119 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 4 | 4 | B.1.438 | 0.026144 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 3 | 3 | AY.44 | 0.000018 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 3 | 3 | B.1.36.16 | 0.004274 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | AY.118 | 0.000125 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | AY.33 | 0.000134 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | AY.9.1 | 0.000167 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | B.1.311 | 0.000549 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | B.1.396 | 0.001411 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 2 | B.1.526 | 0.000024 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 1 | 2 | B.1.526 | 0.000024 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 1 | 2 | B.1.595 | 0.000261 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 2 | B.1.595 | 0.000261 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | B.1.619 | 0.001742 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 2 | 2 | D.2 | 0.00015 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 2 | P.1 | 0.000016 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcG | 1 | 2 | P.1 | 0.000016 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.50 | 0.000799 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.87 | 0.000833 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.90 | 0.000684 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 1 | 1 | B | 0.000128 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.1.263 | 0.001558 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.1.371 | 0.010417 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.1.420 | 0.001006 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.1.54 | 0.003021 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.232 | 0.000537 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcG | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.258.3 | 0.001675 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.439 | 0.005917 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.469 | 0.00361 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 1 | 1 | B.1.567 | 0.003333 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.575.1 | 0.002439 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 1 | 1 | B.1.582 | 0.000491 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.606 | 0.006024 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.620 | 0.000946 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | B.1.9 | 0.006173 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcA | 1 | 1 | B.3 | 0.000831 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | C.14 | 0.004329 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | P.1.17 | 0.000162 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | P.3 | 0.001595 |
ORF1ab/nsp13 | 140 | A140A | gcT | gcC | 1 | 1 | Q.2 | 0.000613 |
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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