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/nsp9 | 15 | A15A | A4155A | syn | gcT | gcG | 890 | 463 | 0.520225 | 12728-12730 |
ORF1ab/nsp9 | 15 | A15A | A4155A | syn | gcT | gcC | 890 | 327 | 0.367416 | 12728-12730 |
ORF1ab/nsp9 | 15 | A15A | A4155A | syn | gcT | gcA | 890 | 100 | 0.11236 | 12728-12730 |
Details of the mutation A15A 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/nsp9 | 15 | A15A | gcT | gcG | 463 | 890 | All | 0.000089 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 327 | 890 | All | 0.000063 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 100 | 890 | All | 0.000019 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 406 | 406 | B.1.625 | 0.955294 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 88 | 124 | B.1.1.7 | 0.000079 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 36 | 124 | B.1.1.7 | 0.000032 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 55 | 62 | AY.4 | 0.000086 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 4 | 62 | AY.4 | 0.000006 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 3 | 62 | AY.4 | 0.000005 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 31 | 37 | B.1 | 0.000284 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 4 | 37 | B.1 | 0.000037 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 2 | 37 | B.1 | 0.000018 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 35 | 36 | B.1.258.17 | 0.003639 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 36 | B.1.258.17 | 0.000104 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 30 | 30 | B.1.2 | 0.000264 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 22 | 25 | AY.103 | 0.000137 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 25 | AY.103 | 0.000012 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 25 | AY.103 | 0.000006 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 12 | 14 | AY.25 | 0.000072 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 2 | 14 | AY.25 | 0.000012 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 7 | 13 | P.1 | 0.00011 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 5 | 13 | P.1 | 0.000079 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 13 | P.1 | 0.000016 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 10 | 11 | B.1.617.2 | 0.000038 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 11 | B.1.617.2 | 0.000004 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 9 | 9 | AY.109 | 0.006657 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 9 | 9 | AY.43 | 0.00004 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 4 | 6 | AY.44 | 0.000024 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 6 | AY.44 | 0.000012 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 4 | 6 | B.1.1 | 0.000073 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 6 | B.1.1 | 0.000036 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 5 | 5 | AY.6 | 0.000206 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 4 | 5 | B.1.617.1 | 0.000516 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 5 | B.1.617.1 | 0.000129 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 4 | 4 | AY.4.2 | 0.000087 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 4 | 4 | B.1.1.374 | 0.009501 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 4 | 4 | B.1.1.70 | 0.001364 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 4 | 4 | B.1.149 | 0.013699 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 3 | 4 | B.1.177 | 0.00004 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 4 | B.1.177 | 0.000013 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 3 | 4 | B.1.429 | 0.000071 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 4 | B.1.429 | 0.000024 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 3 | AY.3 | 0.00002 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 3 | AY.3 | 0.00001 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 3 | 3 | B.4.7 | 0.030303 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 2 | 2 | 0.111111 | |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 2 | AY.102 | 0.000027 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 2 | AY.102 | 0.000027 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 2 | 2 | AY.13 | 0.000322 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 2 | 2 | AY.46.4 | 0.000329 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 2 | AY.57 | 0.001312 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 2 | AY.75 | 0.000056 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 2 | AY.75 | 0.000056 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 2 | B.1.1.337 | 0.007194 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 2 | 2 | B.1.128 | 0.001271 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 2 | B.1.160 | 0.000031 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 2 | B.1.160 | 0.000031 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 2 | 2 | C.37 | 0.000232 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 2 | D.2 | 0.000075 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 2 | D.2 | 0.000075 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 1 | A.23 | 0.010526 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AK.2 | 0.045455 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | AY.29.1 | 0.000221 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | AY.5.4 | 0.000277 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | AZ.3 | 0.00152 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.1.1.174 | 0.003378 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 1 | B.1.1.26 | 0.005236 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.1.1.316 | 0.000925 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 1 | B.1.1.507 | 0.008696 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.1.177.10 | 0.000878 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | B.1.177.18 | 0.00116 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | B.1.177.65 | 0.000665 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 1 | B.1.214.2 | 0.0006 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | B.1.459 | 0.004082 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | B.1.523 | 0.002451 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcG | 1 | 1 | B.1.9 | 0.006173 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | B.6 | 0.00091 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | N.5 | 0.001767 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcC | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp9 | 15 | A15A | gcT | gcA | 1 | 1 | P.1.6 | 0.001946 |
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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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