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 |
S | 694 | A694A | syn | gcC | gcT | 2382 | 2244 | 0.942065 | 23642-23644 | |
S | 694 | A694A | syn | gcC | gcA | 2382 | 136 | 0.0570949 | 23642-23644 | |
S | 694 | A694A | syn | gcC | gcG | 2382 | 2 | 0.000839631 | 23642-23644 |
Details of the mutation A694A 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 |
S | 694 | A694A | gcC | gcT | 2244 | 2382 | All | 0.000429 |
S | 694 | A694A | gcC | gcA | 136 | 2382 | All | 0.000026 |
S | 694 | A694A | gcC | gcG | 2 | 2382 | All | 0 |
S | 694 | A694A | gcC | gcT | 1649 | 1649 | B.1.177.54 | 1 |
S | 694 | A694A | gcC | gcT | 150 | 150 | B.1.177.4 | 0.031659 |
S | 694 | A694A | gcC | gcT | 69 | 91 | B.1.1.7 | 0.000062 |
S | 694 | A694A | gcC | gcA | 22 | 91 | B.1.1.7 | 0.00002 |
S | 694 | A694A | gcC | gcT | 54 | 55 | AY.75 | 0.003025 |
S | 694 | A694A | gcC | gcA | 1 | 55 | AY.75 | 0.000056 |
S | 694 | A694A | gcC | gcT | 44 | 44 | V.1 | 1 |
S | 694 | A694A | gcC | gcT | 41 | 43 | AY.25 | 0.000247 |
S | 694 | A694A | gcC | gcA | 2 | 43 | AY.25 | 0.000012 |
S | 694 | A694A | gcC | gcT | 33 | 35 | AY.4 | 0.000051 |
S | 694 | A694A | gcC | gcA | 2 | 35 | AY.4 | 0.000003 |
S | 694 | A694A | gcC | gcT | 20 | 32 | B.1.617.2 | 0.000075 |
S | 694 | A694A | gcC | gcA | 12 | 32 | B.1.617.2 | 0.000045 |
S | 694 | A694A | gcC | gcT | 31 | 31 | V.2 | 1 |
S | 694 | A694A | gcC | gcA | 16 | 20 | AY.46 | 0.001665 |
S | 694 | A694A | gcC | gcT | 4 | 20 | AY.46 | 0.000416 |
S | 694 | A694A | gcC | gcT | 17 | 17 | B.1.1.311 | 0.006089 |
S | 694 | A694A | gcC | gcA | 8 | 15 | AY.44 | 0.000049 |
S | 694 | A694A | gcC | gcT | 7 | 15 | AY.44 | 0.000043 |
S | 694 | A694A | gcC | gcA | 13 | 14 | AY.3 | 0.000129 |
S | 694 | A694A | gcC | gcT | 1 | 14 | AY.3 | 0.00001 |
S | 694 | A694A | gcC | gcT | 7 | 13 | AY.43 | 0.000031 |
S | 694 | A694A | gcC | gcA | 6 | 13 | AY.43 | 0.000027 |
S | 694 | A694A | gcC | gcT | 9 | 10 | B.1 | 0.000082 |
S | 694 | A694A | gcC | gcA | 1 | 10 | B.1 | 0.000009 |
S | 694 | A694A | gcC | gcT | 9 | 10 | B.1.1 | 0.000163 |
S | 694 | A694A | gcC | gcA | 1 | 10 | B.1.1 | 0.000018 |
S | 694 | A694A | gcC | gcT | 8 | 10 | B.1.177 | 0.000105 |
S | 694 | A694A | gcC | gcA | 2 | 10 | B.1.177 | 0.000026 |
S | 694 | A694A | gcC | gcA | 9 | 9 | AY.46.1 | 0.00924 |
S | 694 | A694A | gcC | gcT | 6 | 6 | AY.102 | 0.000159 |
S | 694 | A694A | gcC | gcT | 6 | 6 | AY.61 | 0.000629 |
S | 694 | A694A | gcC | gcT | 5 | 6 | B.1.2 | 0.000044 |
S | 694 | A694A | gcC | gcA | 1 | 6 | B.1.2 | 0.000009 |
S | 694 | A694A | gcC | gcT | 5 | 5 | AY.26 | 0.000142 |
S | 694 | A694A | gcC | gcT | 3 | 5 | AY.39 | 0.000074 |
S | 694 | A694A | gcC | gcA | 2 | 5 | AY.39 | 0.000049 |
S | 694 | A694A | gcC | gcT | 4 | 5 | B.1.1.519 | 0.000159 |
S | 694 | A694A | gcC | gcA | 1 | 5 | B.1.1.519 | 0.00004 |
S | 694 | A694A | gcC | gcA | 3 | 4 | AY.20 | 0.000117 |
S | 694 | A694A | gcC | gcT | 1 | 4 | AY.20 | 0.000039 |
S | 694 | A694A | gcC | gcT | 4 | 4 | AY.47 | 0.000124 |
S | 694 | A694A | gcC | gcT | 4 | 4 | B.1.1.239 | 0.129032 |
S | 694 | A694A | gcC | gcT | 3 | 4 | B.1.429 | 0.000071 |
S | 694 | A694A | gcC | gcA | 1 | 4 | B.1.429 | 0.000024 |
S | 694 | A694A | gcC | gcT | 2 | 3 | AY.103 | 0.000012 |
S | 694 | A694A | gcC | gcA | 1 | 3 | AY.103 | 0.000006 |
S | 694 | A694A | gcC | gcT | 3 | 3 | AY.120 | 0.000112 |
S | 694 | A694A | gcC | gcT | 3 | 3 | AY.13 | 0.000483 |
S | 694 | A694A | gcC | gcA | 2 | 3 | AY.42 | 0.00008 |
S | 694 | A694A | gcC | gcT | 1 | 3 | AY.42 | 0.00004 |
S | 694 | A694A | gcC | gcA | 3 | 3 | AY.46.2 | 0.001906 |
S | 694 | A694A | gcC | gcA | 2 | 3 | AY.6 | 0.000082 |
S | 694 | A694A | gcC | gcG | 1 | 3 | AY.6 | 0.000041 |
S | 694 | A694A | gcC | gcA | 3 | 3 | AY.62 | 0.001307 |
S | 694 | A694A | gcC | gcA | 2 | 3 | B.1.160 | 0.000062 |
S | 694 | A694A | gcC | gcT | 1 | 3 | B.1.160 | 0.000031 |
S | 694 | A694A | gcC | gcA | 3 | 3 | B.1.9 | 0.018519 |
S | 694 | A694A | gcC | gcT | 2 | 2 | AY.29 | 0.000032 |
S | 694 | A694A | gcC | gcA | 2 | 2 | AY.34 | 0.000194 |
S | 694 | A694A | gcC | gcT | 2 | 2 | AY.46.4 | 0.000329 |
S | 694 | A694A | gcC | gcT | 1 | 2 | AY.9.1 | 0.000084 |
S | 694 | A694A | gcC | gcA | 1 | 2 | AY.9.1 | 0.000084 |
S | 694 | A694A | gcC | gcT | 2 | 2 | AY.98 | 0.000158 |
S | 694 | A694A | gcC | gcA | 2 | 2 | B | 0.000256 |
S | 694 | A694A | gcC | gcA | 1 | 2 | B.1.1.216 | 0.00089 |
S | 694 | A694A | gcC | gcT | 1 | 2 | B.1.1.216 | 0.00089 |
S | 694 | A694A | gcC | gcA | 2 | 2 | B.1.1.28 | 0.000622 |
S | 694 | A694A | gcC | gcT | 2 | 2 | B.1.426 | 0.002018 |
S | 694 | A694A | gcC | gcT | 1 | 2 | P.1 | 0.000016 |
S | 694 | A694A | gcC | gcA | 1 | 2 | P.1 | 0.000016 |
S | 694 | A694A | gcC | gcA | 1 | 1 | AY.113 | 0.000142 |
S | 694 | A694A | gcC | gcT | 1 | 1 | AY.116 | 0.000287 |
S | 694 | A694A | gcC | gcT | 1 | 1 | AY.118 | 0.000063 |
S | 694 | A694A | gcC | gcT | 1 | 1 | AY.119 | 0.000035 |
S | 694 | A694A | gcC | gcT | 1 | 1 | AY.121 | 0.000135 |
S | 694 | A694A | gcC | gcT | 1 | 1 | AY.23 | 0.00007 |
S | 694 | A694A | gcC | gcT | 1 | 1 | AY.39.1 | 0.00004 |
S | 694 | A694A | gcC | gcT | 1 | 1 | AY.4.2 | 0.000022 |
S | 694 | A694A | gcC | gcA | 1 | 1 | AY.4.4 | 0.000409 |
S | 694 | A694A | gcC | gcA | 1 | 1 | AY.67 | 0.000464 |
S | 694 | A694A | gcC | gcA | 1 | 1 | AY.98.1 | 0.000048 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.153 | 0.001095 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.164 | 0.005155 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.214 | 0.000055 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.222 | 0.000204 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.306 | 0.000438 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.318 | 0.000302 |
S | 694 | A694A | gcC | gcA | 1 | 1 | B.1.1.369 | 0.000446 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.434 | 0.000349 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.1.514 | 0.038462 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.139 | 0.000733 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.219 | 0.009434 |
S | 694 | A694A | gcC | gcA | 1 | 1 | B.1.221 | 0.000071 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.243 | 0.00007 |
S | 694 | A694A | gcC | gcA | 1 | 1 | B.1.258.16 | 0.001637 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.319 | 0.003049 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.36.36 | 0.000602 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.509 | 0.000866 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.525 | 0.000113 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.617.1 | 0.000129 |
S | 694 | A694A | gcC | gcT | 1 | 1 | B.1.621 | 0.000089 |
S | 694 | A694A | gcC | gcA | 1 | 1 | B.61 | 0.005747 |
S | 694 | A694A | gcC | gcT | 1 | 1 | P.1.14 | 0.000048 |
S | 694 | A694A | gcC | gcT | 1 | 1 | P.1.17 | 0.000162 |
S | 694 | A694A | gcC | gcT | 1 | 1 | P.7 | 0.004367 |
S | 694 | A694A | gcC | gcG | 1 | 1 | Q.1 | 0.000126 |
S | 694 | A694A | gcC | gcT | 1 | 1 | Q.3 | 0.000145 |
S | 694 | A694A | gcC | gcT | 1 | 1 | U.3 | 0.003861 |
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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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