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 |
M | 3 | D3Y | nonsyn | Gat | Tat | 900 | 900 | 1 | 26529-26531 |
Details of the mutation D3Y 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 |
M | 3 | D3Y | Gat | Tat | 900 | 900 | All | 0.000172 |
M | 3 | D3Y | Gat | Tat | 130 | 130 | B.1.1.7 | 0.000116 |
M | 3 | D3Y | Gat | Tat | 116 | 116 | AY.4 | 0.000181 |
M | 3 | D3Y | Gat | Tat | 62 | 62 | B.1.617.2 | 0.000233 |
M | 3 | D3Y | Gat | Tat | 41 | 41 | AY.43 | 0.000182 |
M | 3 | D3Y | Gat | Tat | 35 | 35 | AY.103 | 0.000217 |
M | 3 | D3Y | Gat | Tat | 25 | 25 | AY.25 | 0.00015 |
M | 3 | D3Y | Gat | Tat | 21 | 21 | AY.44 | 0.000128 |
M | 3 | D3Y | Gat | Tat | 20 | 20 | AY.102 | 0.00053 |
M | 3 | D3Y | Gat | Tat | 19 | 19 | AY.3 | 0.000189 |
M | 3 | D3Y | Gat | Tat | 18 | 18 | AY.27 | 0.001165 |
M | 3 | D3Y | Gat | Tat | 16 | 16 | AY.47 | 0.000498 |
M | 3 | D3Y | Gat | Tat | 15 | 15 | AY.39.1 | 0.000594 |
M | 3 | D3Y | Gat | Tat | 15 | 15 | AY.42 | 0.000603 |
M | 3 | D3Y | Gat | Tat | 15 | 15 | B.1 | 0.000137 |
M | 3 | D3Y | Gat | Tat | 15 | 15 | B.1.2 | 0.000132 |
M | 3 | D3Y | Gat | Tat | 14 | 14 | B.1.561 | 0.005558 |
M | 3 | D3Y | Gat | Tat | 13 | 13 | AY.19 | 0.014823 |
M | 3 | D3Y | Gat | Tat | 11 | 11 | AY.121 | 0.001488 |
M | 3 | D3Y | Gat | Tat | 11 | 11 | AY.39 | 0.000272 |
M | 3 | D3Y | Gat | Tat | 11 | 11 | B.1.1.284 | 0.001181 |
M | 3 | D3Y | Gat | Tat | 11 | 11 | B.1.93 | 0.010271 |
M | 3 | D3Y | Gat | Tat | 10 | 10 | AY.29 | 0.000158 |
M | 3 | D3Y | Gat | Tat | 10 | 10 | B.1.1 | 0.000181 |
M | 3 | D3Y | Gat | Tat | 10 | 10 | C.37 | 0.001161 |
M | 3 | D3Y | Gat | Tat | 9 | 9 | B.1.160 | 0.000281 |
M | 3 | D3Y | Gat | Tat | 9 | 9 | B.1.177 | 0.000119 |
M | 3 | D3Y | Gat | Tat | 8 | 8 | AY.4.2 | 0.000174 |
M | 3 | D3Y | Gat | Tat | 7 | 7 | AY.46.4 | 0.001152 |
M | 3 | D3Y | Gat | Tat | 7 | 7 | B.1.258 | 0.000466 |
M | 3 | D3Y | Gat | Tat | 7 | 7 | P.1 | 0.00011 |
M | 3 | D3Y | Gat | Tat | 6 | 6 | AY.120 | 0.000223 |
M | 3 | D3Y | Gat | Tat | 6 | 6 | AY.4.2.1 | 0.000894 |
M | 3 | D3Y | Gat | Tat | 5 | 5 | AY.5 | 0.000103 |
M | 3 | D3Y | Gat | Tat | 5 | 5 | AY.98.1 | 0.000242 |
M | 3 | D3Y | Gat | Tat | 5 | 5 | B.1.104 | 0.01845 |
M | 3 | D3Y | Gat | Tat | 5 | 5 | B.1.177.16 | 0.003322 |
M | 3 | D3Y | Gat | Tat | 4 | 4 | AY.3.1 | 0.000341 |
M | 3 | D3Y | Gat | Tat | 4 | 4 | B.1.177.4 | 0.000844 |
M | 3 | D3Y | Gat | Tat | 4 | 4 | B.1.329 | 0.00243 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | AY.20 | 0.000117 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | AY.23 | 0.000209 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | AY.4.5 | 0.000322 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | AY.53 | 0.000863 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | AY.7 | 0.000588 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | AY.99.2 | 0.000276 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.1.1 | 0.00098 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.1.129 | 0.027523 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.1.222 | 0.000612 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.1.369 | 0.001339 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.177.21 | 0.000229 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.243 | 0.000209 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.324 | 0.004815 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.351 | 0.000089 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.429 | 0.000071 |
M | 3 | D3Y | Gat | Tat | 3 | 3 | Q.7 | 0.003333 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | 0.111111 | |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.10 | 0.00106 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.119 | 0.000071 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.4.4 | 0.000818 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.46 | 0.000208 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.48 | 0.00093 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.66 | 0.002139 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.68 | 0.000547 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.7.1 | 0.000225 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.74 | 0.000231 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.9 | 0.000135 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | AY.9.1 | 0.000167 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.221 | 0.000142 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.240 | 0.000431 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.526 | 0.000047 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.596 | 0.000174 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.597 | 0.009259 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.617.1 | 0.000258 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.621.1 | 0.001012 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | B.40 | 0.000729 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | P.1.14 | 0.000096 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | P.2 | 0.000373 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | P.3 | 0.00319 |
M | 3 | D3Y | Gat | Tat | 2 | 2 | Q.8 | 0.00033 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | A.2.2 | 0.001689 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.100 | 0.000046 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.101 | 0.00049 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.106 | 0.000335 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.108 | 0.001103 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.110 | 0.000113 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.116.1 | 0.000311 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.117 | 0.000085 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.26 | 0.000028 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.30 | 0.000396 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.36 | 0.000148 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.41 | 0.000294 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.5.3 | 0.000337 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.50 | 0.000799 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.52 | 0.000814 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.54 | 0.000095 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.6 | 0.000041 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.70 | 0.000209 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.75.1 | 0.00018 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.92 | 0.000287 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.95 | 0.000761 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.96 | 0.002075 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | AY.98 | 0.000079 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.214 | 0.000055 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.33 | 0.000421 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.39 | 0.00051 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.519 | 0.00004 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.523 | 0.001563 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.83 | 0.00271 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.13 | 0.002375 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.147 | 0.000756 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.234 | 0.000132 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.279 | 0.000514 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.311 | 0.000275 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.320 | 0.001245 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.36.36 | 0.000602 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.375 | 0.00082 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.400 | 0.000429 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.427 | 0.00005 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.575 | 0.000303 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.576 | 0.000907 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.621 | 0.000089 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.623 | 0.000536 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.637 | 0.000073 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | C.18 | 0.002591 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | D.2 | 0.000075 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | P.1.10 | 0.000269 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | Q.1 | 0.000126 |
M | 3 | D3Y | Gat | Tat | 1 | 1 | R.1 | 0.00009 |
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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