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/nsp1 | 80 | P80P | P80P | syn | ccT | ccC | 1221 | 927 | 0.759214 | 503-505 |
ORF1ab/nsp1 | 80 | P80P | P80P | syn | ccT | ccA | 1221 | 147 | 0.120393 | 503-505 |
ORF1ab/nsp1 | 80 | P80P | P80P | syn | ccT | ccG | 1221 | 147 | 0.120393 | 503-505 |
Details of the mutation P80P 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/nsp1 | 80 | P80P | ccT | ccC | 927 | 1221 | All | 0.000177 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 147 | 1221 | All | 0.000028 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 147 | 1221 | All | 0.000028 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 525 | 525 | B.1.1.198 | 0.770925 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 56 | 130 | B.1.1.7 | 0.00005 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 48 | 130 | B.1.1.7 | 0.000043 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 26 | 130 | B.1.1.7 | 0.000023 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 104 | 125 | B.1.617.2 | 0.000392 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 11 | 125 | B.1.617.2 | 0.000041 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 10 | 125 | B.1.617.2 | 0.000038 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 60 | 66 | AY.43 | 0.000266 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 5 | 66 | AY.43 | 0.000022 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 66 | AY.43 | 0.000004 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 61 | 65 | B.1.2 | 0.000537 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 3 | 65 | B.1.2 | 0.000026 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 65 | B.1.2 | 0.000009 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 38 | 54 | AZ.2 | 0.031199 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 16 | 54 | AZ.2 | 0.013136 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 31 | 40 | AY.44 | 0.000189 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 7 | 40 | AY.44 | 0.000043 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 2 | 40 | AY.44 | 0.000012 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 19 | 21 | C.37 | 0.002205 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 21 | C.37 | 0.000232 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 11 | 11 | B.1.599 | 0.040146 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 9 | 9 | B.1.478 | 0.105882 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 6 | 8 | AY.4 | 0.000009 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 8 | AY.4 | 0.000002 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 8 | AY.4 | 0.000002 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 8 | 8 | AY.5 | 0.000165 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 8 | 8 | B.1.429 | 0.000188 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 7 | 7 | AY.23 | 0.000488 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 5 | 7 | AY.3 | 0.00005 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 7 | AY.3 | 0.00001 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 7 | AY.3 | 0.00001 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 7 | 7 | Q.1 | 0.000884 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 6 | 6 | AY.39 | 0.000148 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 5 | 6 | AY.9.1 | 0.000419 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 6 | AY.9.1 | 0.000084 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 4 | 5 | AY.25 | 0.000024 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 5 | AY.25 | 0.000006 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 5 | P.1 | 0.000032 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 2 | 5 | P.1 | 0.000032 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 5 | P.1 | 0.000016 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 2 | 4 | AY.103 | 0.000012 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 4 | AY.103 | 0.000006 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 4 | AY.103 | 0.000006 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 4 | 4 | AY.120.1 | 0.001284 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 3 | 4 | AY.75.1 | 0.000541 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 4 | AY.75.1 | 0.00018 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 4 | B.1.1.214 | 0.000111 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 2 | 4 | B.1.1.214 | 0.000111 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 3 | 4 | B.1.258 | 0.0002 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 4 | B.1.258 | 0.000067 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 4 | 4 | B.1.258.6 | 0.078431 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 4 | 4 | B.1.637 | 0.000292 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 4 | 4 | C.36.3 | 0.002269 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 2 | 4 | Q.4 | 0.00091 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 2 | 4 | Q.4 | 0.00091 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 4 | 4 | R.1 | 0.00036 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 3 | AY.102 | 0.000053 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 3 | AY.102 | 0.000027 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 3 | AY.119 | 0.000071 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 3 | AY.119 | 0.000035 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 3 | B.1 | 0.000018 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 3 | B.1 | 0.000009 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 3 | B.1.1 | 0.000018 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 3 | B.1.1 | 0.000018 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 3 | B.1.1 | 0.000018 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 2 | AY.19 | 0.002281 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 2 | AY.29 | 0.000016 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 2 | AY.29 | 0.000016 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 2 | AY.34 | 0.000194 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 2 | 2 | AY.34.1 | 0.00102 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 2 | AY.46 | 0.000208 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 2 | AY.46.2 | 0.000635 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 2 | AY.46.2 | 0.000635 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 2 | AY.54 | 0.000191 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | 0.055556 | |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.60 | 0.000938 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.91 | 0.00073 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.1.186 | 0.003436 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.1.294 | 0.001266 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.1.523 | 0.001563 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.1.83 | 0.00271 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.160.16 | 0.000929 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.206 | 0.000816 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.351.3 | 0.000876 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.459 | 0.004082 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.468 | 0.005714 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccG | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.540 | 0.009709 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 1 | P.1.16 | 0.000374 |
ORF1ab/nsp1 | 80 | P80P | ccT | ccA | 1 | 1 | P.1.17 | 0.000162 |
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
|