CoV-GLUE | Mutations | Mutation
CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 273
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/nsp4 | 273 | Q273R | Q3036R | nonsyn | cAa | cGa | 131 | 130 | 0.992366 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273R | Q3036R | nonsyn | cAA | cGG | 131 | 1 | 0.00763359 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273del | Q3036del | del | CAA | --- | 73 | 73 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273Q | Q3036Q | syn | caA | caG | 71 | 71 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273K | Q3036K | nonsyn | Caa | Aaa | 25 | 25 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273X | Q3036X | nonsyn | Caa | Taa | 17 | 17 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273L | Q3036L | nonsyn | cAa | cTa | 10 | 10 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273del1 | Q3036del1 | del | Caa | -aa | 8 | 6 | 0.75 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273del1 | Q3036del1 | del | cAa | c-a | 8 | 2 | 0.25 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273H | Q3036H | nonsyn | caA | caC | 5 | 5 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273E | Q3036E | nonsyn | Caa | Gaa | 2 | 2 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273P | Q3036P | nonsyn | cAa | cCa | 2 | 2 | 1 | 9371-9373 |
| ORF1ab/nsp4 | 273 | Q273del2 | Q3036del2 | del | cAA | c-- | 1 | 1 | 1 | 9371-9373 |
Details of the mutation no 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/nsp4 | 273 | Q273R | cAa | cGa | 130 | 131 | All | 0.000025 |
| ORF1ab/nsp4 | 273 | Q273R | cAA | cGG | 1 | 131 | All | 0 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 73 | 73 | All | 0.000014 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 71 | 71 | All | 0.000014 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 63 | 64 | B.1.1.7 | 0.000056 |
| ORF1ab/nsp4 | 273 | Q273R | cAA | cGG | 1 | 64 | B.1.1.7 | 0.000001 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 32 | 32 | B.1.1.7 | 0.000029 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 25 | 25 | All | 0.000005 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 22 | 22 | B.1.1.7 | 0.00002 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 17 | 17 | All | 0.000003 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 13 | 13 | AY.4 | 0.00002 |
| ORF1ab/nsp4 | 273 | Q273L | cAa | cTa | 10 | 10 | All | 0.000002 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 9 | 9 | AY.9 | 0.000608 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 9 | 9 | B.1.531 | 0.75 |
| ORF1ab/nsp4 | 273 | Q273del1 | Caa | -aa | 6 | 8 | All | 0.000001 |
| ORF1ab/nsp4 | 273 | Q273del1 | cAa | c-a | 2 | 8 | All | 0 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 8 | 8 | AY.44 | 0.000049 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 8 | 8 | B.1.110.3 | 0.005747 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 7 | 7 | AY.4 | 0.000011 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 6 | 6 | AY.25 | 0.000036 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 6 | 6 | AY.9.2 | 0.00022 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 6 | 6 | B.1.427 | 0.000303 |
| ORF1ab/nsp4 | 273 | Q273H | caA | caC | 5 | 5 | All | 0.000001 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 5 | 5 | B.1.1.7 | 0.000004 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 5 | 5 | B.1.177 | 0.000066 |
| ORF1ab/nsp4 | 273 | Q273L | cAa | cTa | 4 | 4 | B.1.1.7 | 0.000004 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 4 | 4 | B.1.617.2 | 0.000015 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 3 | 3 | AY.103 | 0.000019 |
| ORF1ab/nsp4 | 273 | Q273L | cAa | cTa | 3 | 3 | AY.24 | 0.001293 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 3 | 3 | AY.4.5 | 0.000322 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 3 | 3 | B.1 | 0.000027 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 3 | 3 | B.1.1.214 | 0.000166 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 3 | 3 | B.1.177 | 0.00004 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 3 | 3 | B.1.177.4 | 0.000633 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 3 | 3 | B.1.617.2 | 0.000011 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 3 | 3 | B.1.617.2 | 0.000011 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 3 | 3 | P.1 | 0.000047 |
| ORF1ab/nsp4 | 273 | Q273E | Caa | Gaa | 2 | 2 | All | 0 |
| ORF1ab/nsp4 | 273 | Q273P | cAa | cCa | 2 | 2 | All | 0 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 2 | 2 | AY.111 | 0.000366 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 2 | 2 | AY.4 | 0.000003 |
| ORF1ab/nsp4 | 273 | Q273H | caA | caC | 2 | 2 | AY.43 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 2 | 2 | AY.43 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 2 | 2 | AY.43 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 2 | 2 | AY.67 | 0.000929 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 2 | 2 | B.1 | 0.000018 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 2 | 2 | B.1.1 | 0.000036 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 2 | 2 | B.1.1 | 0.000036 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 2 | 2 | B.1.1.317 | 0.000823 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 2 | 2 | B.1.1.7 | 0.000002 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 2 | 2 | B.1.177 | 0.000026 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | A | 0.000387 |
| ORF1ab/nsp4 | 273 | Q273del2 | cAA | c-- | 1 | 1 | All | 0 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 1 | 1 | AY.100 | 0.000046 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | AY.102 | 0.000027 |
| ORF1ab/nsp4 | 273 | Q273L | cAa | cTa | 1 | 1 | AY.102 | 0.000027 |
| ORF1ab/nsp4 | 273 | Q273L | cAa | cTa | 1 | 1 | AY.108 | 0.001103 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | AY.119 | 0.000035 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | AY.120 | 0.000037 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | AY.16 | 0.00038 |
| ORF1ab/nsp4 | 273 | Q273del1 | Caa | -aa | 1 | 1 | AY.25 | 0.000006 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | AY.3 | 0.00001 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | AY.36 | 0.000148 |
| ORF1ab/nsp4 | 273 | Q273del1 | Caa | -aa | 1 | 1 | AY.4.1 | 0.000737 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | AY.4.5 | 0.000107 |
| ORF1ab/nsp4 | 273 | Q273del1 | Caa | -aa | 1 | 1 | AY.4.5 | 0.000107 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 1 | 1 | AY.43 | 0.000004 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | AY.44 | 0.000006 |
| ORF1ab/nsp4 | 273 | Q273H | caA | caC | 1 | 1 | AY.45 | 0.000122 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | AY.46 | 0.000104 |
| ORF1ab/nsp4 | 273 | Q273P | cAa | cCa | 1 | 1 | AY.46.4 | 0.000165 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | AY.47 | 0.000031 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | AY.5 | 0.000021 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | AY.52 | 0.000814 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | AY.6 | 0.000041 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | AY.7 | 0.000196 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | AY.75 | 0.000056 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | AY.9 | 0.000068 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | AY.9 | 0.000068 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | AY.9.2 | 0.000037 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | B | 0.000128 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273del1 | cAa | c-a | 1 | 1 | B.1 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | B.1 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273E | Caa | Gaa | 1 | 1 | B.1 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273H | caA | caC | 1 | 1 | B.1 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.1 | 0.000018 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | B.1.1.153 | 0.001095 |
| ORF1ab/nsp4 | 273 | Q273del1 | Caa | -aa | 1 | 1 | B.1.1.232 | 0.001815 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | B.1.1.291 | 0.000742 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 1 | 1 | B.1.1.298 | 0.000862 |
| ORF1ab/nsp4 | 273 | Q273del1 | Caa | -aa | 1 | 1 | B.1.1.311 | 0.000358 |
| ORF1ab/nsp4 | 273 | Q273L | cAa | cTa | 1 | 1 | B.1.1.311 | 0.000358 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.1.37 | 0.000193 |
| ORF1ab/nsp4 | 273 | Q273E | Caa | Gaa | 1 | 1 | B.1.1.39 | 0.00051 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1.1.519 | 0.00004 |
| ORF1ab/nsp4 | 273 | Q273del1 | Caa | -aa | 1 | 1 | B.1.1.7 | 0.000001 |
| ORF1ab/nsp4 | 273 | Q273P | cAa | cCa | 1 | 1 | B.1.1.7 | 0.000001 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1.160 | 0.000031 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.160 | 0.000031 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | B.1.160 | 0.000031 |
| ORF1ab/nsp4 | 273 | Q273del2 | cAA | c-- | 1 | 1 | B.1.177 | 0.000013 |
| ORF1ab/nsp4 | 273 | Q273H | caA | caC | 1 | 1 | B.1.177 | 0.000013 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.177.17 | 0.000821 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.177.19 | 0.001431 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.177.51 | 0.004566 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.177.54 | 0.000606 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.177.60 | 0.000218 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.177.81 | 0.000189 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 1 | 1 | B.1.2 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.1.2 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | B.1.2 | 0.000009 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | B.1.265 | 0.001271 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 1 | 1 | B.1.329 | 0.000608 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1.427 | 0.00005 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1.429 | 0.000024 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | B.1.429 | 0.000024 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1.507 | 0.011236 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1.596 | 0.000087 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | B.1.617.2 | 0.000004 |
| ORF1ab/nsp4 | 273 | Q273del1 | cAa | c-a | 1 | 1 | B.1.617.2 | 0.000004 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | B.1.623 | 0.000536 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | B.1.637 | 0.000073 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.15 | 0.017544 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | B.4.4 | 0.018868 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | B.6 | 0.00091 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | C.1 | 0.002392 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 1 | 1 | C.35 | 0.000774 |
| ORF1ab/nsp4 | 273 | Q273X | Caa | Taa | 1 | 1 | D.2 | 0.000075 |
| ORF1ab/nsp4 | 273 | Q273K | Caa | Aaa | 1 | 1 | D.2 | 0.000075 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | P.1 | 0.000016 |
| ORF1ab/nsp4 | 273 | Q273Q | caA | caG | 1 | 1 | P.2 | 0.000187 |
| ORF1ab/nsp4 | 273 | Q273del | CAA | --- | 1 | 1 | Q.1 | 0.000126 |
| ORF1ab/nsp4 | 273 | Q273R | cAa | cGa | 1 | 1 | Q.3 | 0.000145 |
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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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