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 | 684 | A684S | nonsyn | Gca | Tca | 1161 | 1161 | 1 | 23612-23614 |
Details of the mutation A684S 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 | 684 | A684S | Gca | Tca | 1161 | 1161 | All | 0.000222 |
S | 684 | A684S | Gca | Tca | 419 | 419 | AY.27 | 0.027118 |
S | 684 | A684S | Gca | Tca | 149 | 149 | AY.44 | 0.000907 |
S | 684 | A684S | Gca | Tca | 110 | 110 | B.1.1.7 | 0.000098 |
S | 684 | A684S | Gca | Tca | 62 | 62 | AY.4 | 0.000096 |
S | 684 | A684S | Gca | Tca | 47 | 47 | B.1.617.2 | 0.000177 |
S | 684 | A684S | Gca | Tca | 35 | 35 | AY.52 | 0.028502 |
S | 684 | A684S | Gca | Tca | 25 | 25 | AY.103 | 0.000155 |
S | 684 | A684S | Gca | Tca | 21 | 21 | AY.102 | 0.000557 |
S | 684 | A684S | Gca | Tca | 17 | 17 | AY.25 | 0.000102 |
S | 684 | A684S | Gca | Tca | 15 | 15 | B.1 | 0.000137 |
S | 684 | A684S | Gca | Tca | 13 | 13 | D.2 | 0.000976 |
S | 684 | A684S | Gca | Tca | 12 | 12 | AY.16.1 | 0.005639 |
S | 684 | A684S | Gca | Tca | 12 | 12 | AY.3 | 0.000119 |
S | 684 | A684S | Gca | Tca | 11 | 11 | AY.43 | 0.000049 |
S | 684 | A684S | Gca | Tca | 9 | 9 | AY.120 | 0.000335 |
S | 684 | A684S | Gca | Tca | 9 | 9 | B.1.1 | 0.000163 |
S | 684 | A684S | Gca | Tca | 7 | 7 | AY.118 | 0.000439 |
S | 684 | A684S | Gca | Tca | 7 | 7 | AY.39 | 0.000173 |
S | 684 | A684S | Gca | Tca | 7 | 7 | AY.46 | 0.000729 |
S | 684 | A684S | Gca | Tca | 7 | 7 | AY.46.4 | 0.001152 |
S | 684 | A684S | Gca | Tca | 7 | 7 | B.1.1.519 | 0.000278 |
S | 684 | A684S | Gca | Tca | 6 | 6 | AY.111 | 0.001099 |
S | 684 | A684S | Gca | Tca | 6 | 6 | AY.4.5 | 0.000645 |
S | 684 | A684S | Gca | Tca | 6 | 6 | B.1.427 | 0.000303 |
S | 684 | A684S | Gca | Tca | 6 | 6 | B.1.429 | 0.000141 |
S | 684 | A684S | Gca | Tca | 5 | 5 | AY.26 | 0.000142 |
S | 684 | A684S | Gca | Tca | 5 | 5 | B.1.1.335 | 0.064935 |
S | 684 | A684S | Gca | Tca | 5 | 5 | B.1.2 | 0.000044 |
S | 684 | A684S | Gca | Tca | 5 | 5 | P.1 | 0.000079 |
S | 684 | A684S | Gca | Tca | 4 | 4 | AY.117 | 0.000338 |
S | 684 | A684S | Gca | Tca | 4 | 4 | AY.33 | 0.000267 |
S | 684 | A684S | Gca | Tca | 4 | 4 | AY.46.1 | 0.004107 |
S | 684 | A684S | Gca | Tca | 4 | 4 | AY.47 | 0.000124 |
S | 684 | A684S | Gca | Tca | 4 | 4 | AY.62 | 0.001743 |
S | 684 | A684S | Gca | Tca | 4 | 4 | AY.98.1 | 0.000194 |
S | 684 | A684S | Gca | Tca | 4 | 4 | B.1.351 | 0.000119 |
S | 684 | A684S | Gca | Tca | 4 | 4 | P.2 | 0.000747 |
S | 684 | A684S | Gca | Tca | 4 | 4 | R.1 | 0.00036 |
S | 684 | A684S | Gca | Tca | 3 | 3 | AY.100 | 0.000138 |
S | 684 | A684S | Gca | Tca | 3 | 3 | AY.61 | 0.000314 |
S | 684 | A684S | Gca | Tca | 3 | 3 | B.1.160.32 | 0.012876 |
S | 684 | A684S | Gca | Tca | 2 | 2 | A.2.5.1 | 0.009615 |
S | 684 | A684S | Gca | Tca | 2 | 2 | AY.113 | 0.000285 |
S | 684 | A684S | Gca | Tca | 2 | 2 | AY.39.2 | 0.003082 |
S | 684 | A684S | Gca | Tca | 2 | 2 | AY.4.2 | 0.000043 |
S | 684 | A684S | Gca | Tca | 2 | 2 | AY.41 | 0.000588 |
S | 684 | A684S | Gca | Tca | 2 | 2 | AY.5 | 0.000041 |
S | 684 | A684S | Gca | Tca | 2 | 2 | AY.70 | 0.000417 |
S | 684 | A684S | Gca | Tca | 2 | 2 | B.1.1.39 | 0.001019 |
S | 684 | A684S | Gca | Tca | 2 | 2 | B.1.177 | 0.000026 |
S | 684 | A684S | Gca | Tca | 2 | 2 | B.1.596 | 0.000174 |
S | 684 | A684S | Gca | Tca | 1 | 1 | A | 0.000387 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.121 | 0.000135 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.20 | 0.000039 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.23 | 0.00007 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.29 | 0.000016 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.35 | 0.000233 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.36 | 0.000148 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.48 | 0.000465 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.50 | 0.000799 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.59 | 0.00053 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.6 | 0.000041 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.60 | 0.000938 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.67 | 0.000464 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.68 | 0.000274 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.7 | 0.000196 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.7.1 | 0.000113 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.74 | 0.000116 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.75 | 0.000056 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.78 | 0.001541 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.8 | 0.000606 |
S | 684 | A684S | Gca | Tca | 1 | 1 | AY.99.2 | 0.000092 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B | 0.000128 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.222 | 0.000204 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.25 | 0.000569 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.28 | 0.000311 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.284 | 0.000107 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.318 | 0.000302 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.33 | 0.000421 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.369 | 0.000446 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.377 | 0.001381 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.50 | 0.000679 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.1.526 | 0.003546 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.160 | 0.000031 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.177.35 | 0.000691 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.177.43 | 0.001477 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.177.54 | 0.000606 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.177.73 | 0.000566 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.242 | 0.018868 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.349 | 0.000715 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.391 | 0.001127 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.404 | 0.001302 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.416 | 0.001269 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.428 | 0.00102 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.501 | 0.007353 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.620 | 0.000946 |
S | 684 | A684S | Gca | Tca | 1 | 1 | B.1.628 | 0.000352 |
S | 684 | A684S | Gca | Tca | 1 | 1 | C.40 | 0.027778 |
S | 684 | A684S | Gca | Tca | 1 | 1 | D.3 | 0.005917 |
S | 684 | A684S | Gca | Tca | 1 | 1 | P.1.15 | 0.000232 |
S | 684 | A684S | Gca | Tca | 1 | 1 | P.1.16 | 0.000374 |
S | 684 | A684S | Gca | Tca | 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
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