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 |
ORF1ab/nsp2 | 39 | L39L | L219L | syn | ctG | ctT | 11141 | 1825 | 0.163809 | 920-922 |
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/nsp2 | 39 | L39L | ctG | ctT | 1825 | 11141 | All | 0.000349 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 165 | 1898 | B.1.1.7 | 0.000148 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 112 | 627 | AY.4 | 0.000174 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 561 | D.2 | 0.00015 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 25 | 418 | AY.44 | 0.000152 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 176 | 411 | B.1.617.2 | 0.000663 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 4 | 403 | B.1.429 | 0.000094 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 8 | 323 | B.1.36 | 0.001167 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 60 | 318 | AY.103 | 0.000373 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 161 | 266 | P.1 | 0.002536 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 242 | 250 | AY.98.1 | 0.01172 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 248 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 25 | 228 | B.1.2 | 0.00022 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 13 | 212 | B.1.177 | 0.000171 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 31 | 179 | B.1 | 0.000284 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 8 | 159 | AY.120 | 0.000297 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 150 | 150 | C.2.1 | 1 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 36 | 141 | AY.3 | 0.000358 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 14 | 117 | B.1.637 | 0.001023 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 44 | 115 | AY.43 | 0.000195 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 86 | 114 | B.1.596 | 0.007494 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 9 | 102 | B.1.1 | 0.000163 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 6 | 73 | B.1.160 | 0.000187 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 71 | AY.20 | 0.000117 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 66 | B.1.1.214 | 0.000055 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 62 | C.16 | 0.002121 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 25 | 55 | AY.39 | 0.000618 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 7 | 54 | AY.39.1 | 0.000277 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 9 | 51 | AY.25 | 0.000054 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 8 | 50 | B.1.526 | 0.000188 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 27 | 49 | AY.102 | 0.000716 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 49 | AY.99.2 | 0.000184 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 48 | AY.47 | 0.000062 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 24 | 41 | Q.3 | 0.003481 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 5 | 39 | AY.5 | 0.000103 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 38 | AY.100 | 0.000092 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 37 | AY.36 | 0.000148 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 9 | 35 | AY.26 | 0.000255 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 34 | AY.9.1 | 0.000084 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 33 | AY.29 | 0.000016 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 4 | 33 | B.1.351 | 0.000119 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 31 | 31 | C.2 | 0.5 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 7 | 30 | AY.61 | 0.000733 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 24 | 29 | AY.33 | 0.001603 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 4 | 28 | B.1.221 | 0.000284 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 26 | B.1.1.519 | 0.000119 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 26 | B.1.427 | 0.00005 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 22 | AY.121 | 0.000406 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 21 | AY.4.2 | 0.000022 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 21 | 21 | B.1.177.16 | 0.013953 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 7 | 21 | P.1.14 | 0.000335 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 15 | AY.75.1 | 0.000361 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 14 | 15 | B.1.1.434 | 0.00488 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 11 | 14 | AY.23 | 0.000767 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 14 | 14 | B.1.1.155 | 1 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 13 | AY.9 | 0.000135 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 9 | 13 | B.1.1.1 | 0.00294 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 6 | 12 | AY.9.2 | 0.00022 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 12 | B.1.240 | 0.000647 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 12 | B.1.499 | 0.00105 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 10 | 11 | AY.106 | 0.003349 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 10 | 11 | B.1.1.306 | 0.004384 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 10 | 10 | B.1.177.69 | 0.014837 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 4 | 9 | AY.29.1 | 0.000882 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 9 | B.1.369 | 0.000856 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 8 | B.1.258.17 | 0.000208 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 8 | 8 | P.6 | 0.025157 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 7 | AY.119 | 0.000071 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 7 | AY.34 | 0.000194 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 7 | AY.46 | 0.000312 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 6 | 7 | AY.5.4 | 0.00166 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 7 | AY.6 | 0.000041 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 7 | AY.75 | 0.000112 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 6 | 7 | B.1.236 | 0.01232 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 7 | B.1.36.29 | 0.000517 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 7 | Q.1 | 0.000126 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 6 | AY.118 | 0.000188 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 6 | B.1.438 | 0.013072 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 5 | AY.117 | 0.000169 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 5 | B.1.1.25 | 0.001137 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 5 | B.1.1.277 | 0.000759 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 5 | B.1.1.284 | 0.000322 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 4 | AY.24 | 0.000862 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 4 | AY.3.1 | 0.000085 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 4 | AY.77 | 0.003382 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 4 | B.1.1.216 | 0.00089 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 4 | 4 | B.1.1.222 | 0.000816 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 4 | B.1.177.21 | 0.000153 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 4 | B.1.234 | 0.000264 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 3 | AY.109 | 0.001479 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 3 | AY.13 | 0.000161 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 3 | AY.16.1 | 0.00047 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 3 | AY.34.1 | 0.00153 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 3 | AY.35 | 0.000233 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 3 | 3 | AY.46.3 | 0.002801 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 3 | AY.46.6 | 0.000144 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 3 | AY.5.3 | 0.000337 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 3 | B.1.1.33 | 0.000421 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 3 | B.1.466.2 | 0.000391 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 2 | B.1.1.189 | 0.001513 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 2 | B.1.1.311 | 0.000358 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 2 | B.1.1.54 | 0.003021 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 2 | B.1.147 | 0.001512 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 2 | B.1.177.60 | 0.000437 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 2 | B.1.375 | 0.001639 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 2 | B.1.527 | 0.007407 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 2 | B.1.617.1 | 0.000129 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 2 | P.1.1 | 0.000318 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 2 | 2 | P.1.8 | 0.009569 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | A.2.3 | 0.004739 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | AY.105 | 0.000643 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | AY.115 | 0.005208 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | AY.46.1 | 0.001027 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | AY.7.2 | 0.000559 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | AY.70 | 0.000209 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.1.203 | 0.016949 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.1.526 | 0.003546 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.177.48 | 0.003125 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.229 | 0.009709 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.428 | 0.00102 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.495 | 0.009091 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.540 | 0.009709 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.570 | 0.002941 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 1 | 1 | P.1.10.2 | 0.041667 |
ORF1ab/nsp2 | 39 | L39L | ctG | ctT | 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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