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 |
ORF3a | 57 | Q57R | nonsyn | cAg | cGg | 2749 | 2592 | 0.942888 | 25561-25563 | |
ORF3a | 57 | Q57R | nonsyn | cAG | cGT | 2749 | 156 | 0.0567479 | 25561-25563 | |
ORF3a | 57 | Q57R | nonsyn | CAg | AGg | 2749 | 1 | 0.000363769 | 25561-25563 |
Details of the mutation Q57R 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 |
ORF3a | 57 | Q57R | cAg | cGg | 2592 | 2749 | All | 0.000496 |
ORF3a | 57 | Q57R | cAG | cGT | 156 | 2749 | All | 0.00003 |
ORF3a | 57 | Q57R | CAg | AGg | 1 | 2749 | All | 0 |
ORF3a | 57 | Q57R | cAg | cGg | 950 | 950 | AY.51 | 0.863636 |
ORF3a | 57 | Q57R | cAg | cGg | 844 | 846 | B.1.617.2 | 0.003178 |
ORF3a | 57 | Q57R | cAG | cGT | 2 | 846 | B.1.617.2 | 0.000008 |
ORF3a | 57 | Q57R | cAg | cGg | 214 | 215 | AY.4 | 0.000333 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 215 | AY.4 | 0.000002 |
ORF3a | 57 | Q57R | cAG | cGT | 110 | 191 | AY.19 | 0.125428 |
ORF3a | 57 | Q57R | cAg | cGg | 81 | 191 | AY.19 | 0.09236 |
ORF3a | 57 | Q57R | cAg | cGg | 87 | 87 | AY.17 | 0.713115 |
ORF3a | 57 | Q57R | cAg | cGg | 73 | 73 | AY.16.1 | 0.034305 |
ORF3a | 57 | Q57R | cAg | cGg | 42 | 42 | B.1.1.7 | 0.000038 |
ORF3a | 57 | Q57R | cAg | cGg | 40 | 40 | AY.44 | 0.000243 |
ORF3a | 57 | Q57R | cAg | cGg | 38 | 39 | AY.43 | 0.000168 |
ORF3a | 57 | Q57R | CAg | AGg | 1 | 39 | AY.43 | 0.000004 |
ORF3a | 57 | Q57R | cAg | cGg | 20 | 20 | AY.75 | 0.00112 |
ORF3a | 57 | Q57R | cAg | cGg | 16 | 16 | AY.9.2 | 0.000588 |
ORF3a | 57 | Q57R | cAg | cGg | 10 | 14 | B.1 | 0.000092 |
ORF3a | 57 | Q57R | cAG | cGT | 4 | 14 | B.1 | 0.000037 |
ORF3a | 57 | Q57R | cAg | cGg | 13 | 13 | AY.39 | 0.000321 |
ORF3a | 57 | Q57R | cAg | cGg | 13 | 13 | AY.68 | 0.003559 |
ORF3a | 57 | Q57R | cAg | cGg | 10 | 10 | AY.55 | 0.009174 |
ORF3a | 57 | Q57R | cAG | cGT | 10 | 10 | B.1.2 | 0.000088 |
ORF3a | 57 | Q57R | cAg | cGg | 9 | 9 | AY.102 | 0.000239 |
ORF3a | 57 | Q57R | cAg | cGg | 8 | 8 | AY.13 | 0.001288 |
ORF3a | 57 | Q57R | cAg | cGg | 8 | 8 | AY.37 | 0.002528 |
ORF3a | 57 | Q57R | cAg | cGg | 8 | 8 | AY.65 | 0.004264 |
ORF3a | 57 | Q57R | cAg | cGg | 8 | 8 | AY.9.1 | 0.00067 |
ORF3a | 57 | Q57R | cAg | cGg | 6 | 7 | AY.47 | 0.000187 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 7 | AY.47 | 0.000031 |
ORF3a | 57 | Q57R | cAG | cGT | 7 | 7 | B.1.351 | 0.000208 |
ORF3a | 57 | Q57R | cAg | cGg | 5 | 6 | AY.45 | 0.000608 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 6 | AY.45 | 0.000122 |
ORF3a | 57 | Q57R | cAG | cGT | 6 | 6 | B.1.160 | 0.000187 |
ORF3a | 57 | Q57R | cAG | cGT | 6 | 6 | B.1.40 | 0.117647 |
ORF3a | 57 | Q57R | cAg | cGg | 5 | 5 | AY.10 | 0.00265 |
ORF3a | 57 | Q57R | cAg | cGg | 4 | 5 | AY.52 | 0.003257 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 5 | AY.52 | 0.000814 |
ORF3a | 57 | Q57R | cAg | cGg | 5 | 5 | AY.67 | 0.002321 |
ORF3a | 57 | Q57R | cAg | cGg | 5 | 5 | AY.98 | 0.000395 |
ORF3a | 57 | Q57R | cAg | cGg | 4 | 4 | AY.100 | 0.000184 |
ORF3a | 57 | Q57R | cAg | cGg | 3 | 3 | AY.23 | 0.000209 |
ORF3a | 57 | Q57R | cAg | cGg | 3 | 3 | AY.38 | 0.001498 |
ORF3a | 57 | Q57R | cAg | cGg | 3 | 3 | AY.40 | 0.002893 |
ORF3a | 57 | Q57R | cAg | cGg | 3 | 3 | AY.54 | 0.000286 |
ORF3a | 57 | Q57R | cAg | cGg | 3 | 3 | B.1.1 | 0.000054 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.110 | 0.000225 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.117 | 0.000169 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 2 | AY.120 | 0.000037 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 2 | AY.120 | 0.000037 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.25 | 0.000012 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.30 | 0.000791 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.42 | 0.00008 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.46 | 0.000208 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.49 | 0.00639 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.5.4 | 0.000553 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.73 | 0.001331 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.75.1 | 0.000361 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | AY.98.1 | 0.000097 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 2 | B.1.177 | 0.000013 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 2 | B.1.177 | 0.000013 |
ORF3a | 57 | Q57R | cAg | cGg | 2 | 2 | P.1.13 | 0.001797 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.101 | 0.00049 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.103 | 0.000006 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.121 | 0.000135 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.14 | 0.000088 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.16 | 0.00038 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.20 | 0.000039 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.24 | 0.000431 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.26 | 0.000028 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.3 | 0.00001 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.33 | 0.000067 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.4.5 | 0.000107 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.46.2 | 0.000635 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.46.6 | 0.000072 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.5 | 0.000021 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.59 | 0.00053 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.61 | 0.000105 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.7.1 | 0.000113 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.82 | 0.001357 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.91 | 0.00073 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.93 | 0.000273 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | AY.99.1 | 0.001553 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | B.1.1.228 | 0.003049 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 1 | B.1.1.372 | 0.000689 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | B.1.177.73 | 0.000566 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | B.1.210 | 0.002132 |
ORF3a | 57 | Q57R | cAg | cGg | 1 | 1 | B.1.221 | 0.000071 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 1 | B.1.369 | 0.000285 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 1 | B.1.429 | 0.000024 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 1 | B.1.459 | 0.004082 |
ORF3a | 57 | Q57R | cAG | cGT | 1 | 1 | B.1.466.2 | 0.000391 |
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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