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 | 1140 | P1140P | syn | ccT | ccC | 1665 | 1349 | 0.81021 | 24980-24982 | |
S | 1140 | P1140P | syn | ccT | ccG | 1665 | 276 | 0.165766 | 24980-24982 | |
S | 1140 | P1140P | syn | ccT | ccA | 1665 | 40 | 0.024024 | 24980-24982 |
Details of the mutation P1140P 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 | 1140 | P1140P | ccT | ccC | 1349 | 1665 | All | 0.000258 |
S | 1140 | P1140P | ccT | ccG | 276 | 1665 | All | 0.000053 |
S | 1140 | P1140P | ccT | ccA | 40 | 1665 | All | 0.000008 |
S | 1140 | P1140P | ccT | ccC | 988 | 988 | B.1 | 0.00905 |
S | 1140 | P1140P | ccT | ccG | 203 | 215 | B.1.617.2 | 0.000764 |
S | 1140 | P1140P | ccT | ccC | 9 | 215 | B.1.617.2 | 0.000034 |
S | 1140 | P1140P | ccT | ccA | 3 | 215 | B.1.617.2 | 0.000011 |
S | 1140 | P1140P | ccT | ccC | 63 | 63 | B.1.569 | 0.913043 |
S | 1140 | P1140P | ccT | ccC | 61 | 61 | B.1.521 | 0.303483 |
S | 1140 | P1140P | ccT | ccG | 43 | 43 | AY.98 | 0.003397 |
S | 1140 | P1140P | ccT | ccC | 28 | 31 | AY.4 | 0.000044 |
S | 1140 | P1140P | ccT | ccA | 2 | 31 | AY.4 | 0.000003 |
S | 1140 | P1140P | ccT | ccG | 1 | 31 | AY.4 | 0.000002 |
S | 1140 | P1140P | ccT | ccC | 20 | 26 | B.1.1.7 | 0.000018 |
S | 1140 | P1140P | ccT | ccG | 4 | 26 | B.1.1.7 | 0.000004 |
S | 1140 | P1140P | ccT | ccA | 2 | 26 | B.1.1.7 | 0.000002 |
S | 1140 | P1140P | ccT | ccC | 19 | 19 | B.1.2 | 0.000167 |
S | 1140 | P1140P | ccT | ccC | 12 | 19 | B.1.526 | 0.000282 |
S | 1140 | P1140P | ccT | ccA | 7 | 19 | B.1.526 | 0.000165 |
S | 1140 | P1140P | ccT | ccA | 11 | 11 | AY.4.2 | 0.000239 |
S | 1140 | P1140P | ccT | ccC | 9 | 10 | AY.103 | 0.000056 |
S | 1140 | P1140P | ccT | ccA | 1 | 10 | AY.103 | 0.000006 |
S | 1140 | P1140P | ccT | ccC | 10 | 10 | AY.26 | 0.000283 |
S | 1140 | P1140P | ccT | ccG | 7 | 10 | AY.3 | 0.00007 |
S | 1140 | P1140P | ccT | ccC | 3 | 10 | AY.3 | 0.00003 |
S | 1140 | P1140P | ccT | ccC | 8 | 10 | AY.44 | 0.000049 |
S | 1140 | P1140P | ccT | ccG | 2 | 10 | AY.44 | 0.000012 |
S | 1140 | P1140P | ccT | ccC | 9 | 9 | B.1.76 | 0.102273 |
S | 1140 | P1140P | ccT | ccC | 8 | 8 | AY.27 | 0.000518 |
S | 1140 | P1140P | ccT | ccC | 6 | 6 | AE.8 | 0.002934 |
S | 1140 | P1140P | ccT | ccA | 3 | 6 | AY.102 | 0.00008 |
S | 1140 | P1140P | ccT | ccC | 3 | 6 | AY.102 | 0.00008 |
S | 1140 | P1140P | ccT | ccC | 5 | 6 | B.1.1 | 0.000091 |
S | 1140 | P1140P | ccT | ccG | 1 | 6 | B.1.1 | 0.000018 |
S | 1140 | P1140P | ccT | ccG | 5 | 5 | B.1.36 | 0.00073 |
S | 1140 | P1140P | ccT | ccC | 5 | 5 | B.1.438.1 | 0.000536 |
S | 1140 | P1140P | ccT | ccC | 4 | 4 | AY.25 | 0.000024 |
S | 1140 | P1140P | ccT | ccG | 3 | 4 | AY.32 | 0.001597 |
S | 1140 | P1140P | ccT | ccA | 1 | 4 | AY.32 | 0.000532 |
S | 1140 | P1140P | ccT | ccC | 4 | 4 | B.1.177 | 0.000053 |
S | 1140 | P1140P | ccT | ccC | 4 | 4 | B.1.429 | 0.000094 |
S | 1140 | P1140P | ccT | ccC | 4 | 4 | B.1.9.5 | 0.022727 |
S | 1140 | P1140P | ccT | ccA | 3 | 3 | 0.166667 | |
S | 1140 | P1140P | ccT | ccC | 2 | 3 | AY.43 | 0.000009 |
S | 1140 | P1140P | ccT | ccA | 1 | 3 | AY.43 | 0.000004 |
S | 1140 | P1140P | ccT | ccC | 3 | 3 | AY.54 | 0.000286 |
S | 1140 | P1140P | ccT | ccC | 3 | 3 | B.1.284 | 0.039474 |
S | 1140 | P1140P | ccT | ccC | 3 | 3 | B.1.621 | 0.000266 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | AY.100 | 0.000092 |
S | 1140 | P1140P | ccT | ccA | 2 | 2 | AY.118 | 0.000125 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | AY.45 | 0.000243 |
S | 1140 | P1140P | ccT | ccC | 1 | 2 | AY.5 | 0.000021 |
S | 1140 | P1140P | ccT | ccG | 1 | 2 | AY.5 | 0.000021 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | AY.99.2 | 0.000184 |
S | 1140 | P1140P | ccT | ccG | 2 | 2 | B.1.1.174 | 0.006757 |
S | 1140 | P1140P | ccT | ccA | 2 | 2 | B.1.1.306 | 0.000877 |
S | 1140 | P1140P | ccT | ccG | 2 | 2 | B.1.177.81 | 0.000379 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | B.1.243 | 0.000139 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | B.1.36.8 | 0.002 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | B.1.396 | 0.001411 |
S | 1140 | P1140P | ccT | ccG | 1 | 2 | B.3 | 0.000831 |
S | 1140 | P1140P | ccT | ccC | 1 | 2 | B.3 | 0.000831 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | D.2 | 0.00015 |
S | 1140 | P1140P | ccT | ccC | 2 | 2 | P.1 | 0.000032 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | A.2 | 0.000662 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.105 | 0.000643 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.117 | 0.000085 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.119 | 0.000035 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.12 | 0.000316 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.120 | 0.000037 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.20 | 0.000039 |
S | 1140 | P1140P | ccT | ccA | 1 | 1 | AY.23 | 0.00007 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.29 | 0.000016 |
S | 1140 | P1140P | ccT | ccG | 1 | 1 | AY.39 | 0.000025 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.39.1 | 0.00004 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.39.1.1 | 0.000725 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.74 | 0.000116 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | AY.9.1 | 0.000084 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B | 0.000128 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.1.1 | 0.000327 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.1.123 | 0.017857 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.1.194 | 0.00495 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.1.222 | 0.000204 |
S | 1140 | P1140P | ccT | ccA | 1 | 1 | B.1.160 | 0.000031 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.177.56 | 0.000668 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.206 | 0.000816 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.221 | 0.000071 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.298 | 0.002114 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.311 | 0.000275 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.324 | 0.001605 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.361 | 0.001289 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.367 | 0.000792 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.370 | 0.008 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.377 | 0.004566 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.413 | 0.004255 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.438 | 0.006536 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.452 | 0.013699 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.459 | 0.004082 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.501 | 0.007353 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.575 | 0.000303 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.577 | 0.000687 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.88.1 | 0.004808 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | B.1.94 | 0.027027 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | N.4 | 0.004255 |
S | 1140 | P1140P | ccT | ccC | 1 | 1 | P.1.16 | 0.000374 |
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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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