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/nsp3 | 558 | R558R | R1376R | syn | Cga | Aga | 1059 | 456 | 0.430595 | 4391-4393 |
ORF1ab/nsp3 | 558 | R558R | R1376R | syn | cgA | cgC | 1059 | 373 | 0.352219 | 4391-4393 |
ORF1ab/nsp3 | 558 | R558R | R1376R | syn | cgA | cgG | 1059 | 210 | 0.1983 | 4391-4393 |
ORF1ab/nsp3 | 558 | R558R | R1376R | syn | cgA | cgT | 1059 | 20 | 0.0188857 | 4391-4393 |
Details of the mutation R558R 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/nsp3 | 558 | R558R | Cga | Aga | 456 | 1059 | All | 0.000087 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 373 | 1059 | All | 0.000071 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 210 | 1059 | All | 0.00004 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 20 | 1059 | All | 0.000004 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 312 | 312 | B.1.1.253 | 0.781955 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 188 | 224 | AY.4 | 0.000293 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 22 | 224 | AY.4 | 0.000034 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 14 | 224 | AY.4 | 0.000022 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 80 | 94 | B.1.1.7 | 0.000072 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 8 | 94 | B.1.1.7 | 0.000007 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 5 | 94 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 94 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 80 | 80 | AY.29 | 0.001262 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 54 | 55 | AY.39 | 0.001334 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 55 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 17 | 44 | B.1.617.2 | 0.000064 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 12 | 44 | B.1.617.2 | 0.000045 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 10 | 44 | B.1.617.2 | 0.000038 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 5 | 44 | B.1.617.2 | 0.000019 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 17 | 29 | AY.25 | 0.000102 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 11 | 29 | AY.25 | 0.000066 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 29 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 24 | 24 | B.1.177 | 0.000316 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 7 | 15 | AY.43 | 0.000031 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 5 | 15 | AY.43 | 0.000022 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 3 | 15 | AY.43 | 0.000013 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 12 | 13 | AY.75 | 0.000672 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 13 | AY.75 | 0.000056 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 12 | 12 | AY.27 | 0.000777 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 5 | 12 | B.1 | 0.000046 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 4 | 12 | B.1 | 0.000037 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 3 | 12 | B.1 | 0.000027 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 11 | 11 | AY.118 | 0.000689 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 7 | 9 | B.1.1 | 0.000127 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 2 | 9 | B.1.1 | 0.000036 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 8 | 9 | P.1 | 0.000126 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 9 | P.1 | 0.000016 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 7 | 8 | AY.23 | 0.000488 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 8 | AY.23 | 0.00007 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 5 | 8 | B.1.2 | 0.000044 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 2 | 8 | B.1.2 | 0.000018 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 8 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 7 | 7 | AY.46 | 0.000729 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 3 | 6 | AY.44 | 0.000018 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 3 | 6 | AY.44 | 0.000018 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 5 | 5 | B.1.177.35 | 0.003455 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 4 | 4 | AY.29.1 | 0.000882 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 2 | 4 | AY.3 | 0.00002 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 4 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 4 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 2 | 3 | AY.100 | 0.000092 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 3 | AY.100 | 0.000046 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 2 | 3 | AY.102 | 0.000053 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 3 | AY.102 | 0.000027 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 3 | 3 | AY.103 | 0.000019 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 2 | 3 | AY.119 | 0.000071 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 3 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 3 | 3 | AY.34 | 0.000291 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 3 | 3 | B.1.177.40 | 0.015464 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 2 | 3 | B.1.351 | 0.000059 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 3 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 2 | 2 | AY.14 | 0.000176 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 2 | 2 | AY.46.4 | 0.000329 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 2 | 2 | B.1.1.58 | 0.010753 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 2 | B.1.160 | 0.000031 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 2 | B.1.160 | 0.000031 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 2 | B.1.177.16 | 0.000664 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 2 | B.1.177.16 | 0.000664 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 2 | B.1.36 | 0.000146 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 2 | B.1.36 | 0.000146 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 2 | 2 | B.1.525 | 0.000226 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 2 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 2 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 2 | 2 | Q.1 | 0.000253 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | A.2.4 | 0.003367 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | AY.46.5 | 0.000198 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | AY.70 | 0.000209 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | AY.73 | 0.000665 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | AY.91 | 0.00073 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | B.1.1.210 | 0.005714 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | B.1.160.16 | 0.000929 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | B.1.351.3 | 0.000876 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | B.1.381 | 0.007812 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | B.1.391 | 0.001127 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 1 | B.1.420 | 0.010417 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | B.1.459 | 0.004082 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgT | 1 | 1 | B.1.480 | 0.002488 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgC | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp3 | 558 | R558R | cgA | cgG | 1 | 1 | N.3 | 0.005814 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | N.5 | 0.001767 |
ORF1ab/nsp3 | 558 | R558R | Cga | Aga | 1 | 1 | P.1.1 | 0.000318 |
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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