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/nsp5A-B | 96 | P96L | P3359L | nonsyn | cCt | cTt | 5093 | 5092 | 0.999804 | 10340-10342 |
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/nsp5A-B | 96 | P96L | cCt | cTt | 5092 | 5093 | All | 0.000974 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1376 | 1376 | B.1.400 | 0.590305 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1041 | 1041 | B.1.1.7 | 0.000932 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 722 | 722 | AY.25 | 0.004343 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 407 | 407 | B.1.1 | 0.007383 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 308 | 308 | B.1 | 0.002821 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 169 | 169 | B.1.526 | 0.003972 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 116 | 116 | AY.4 | 0.000181 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 91 | 91 | R.1 | 0.008191 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 69 | 69 | P.1 | 0.001087 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 63 | 63 | B.1.400.1 | 0.954545 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 61 | 61 | B.1.1.214 | 0.003383 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 45 | 45 | B.1.617.2 | 0.000169 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 28 | 28 | AY.39 | 0.000692 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 27 | 27 | B.1.2 | 0.000238 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 24 | 24 | AY.44 | 0.000146 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 24 | 24 | B.1.1.419 | 0.177778 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 21 | 21 | AY.103 | 0.00013 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 21 | 21 | B.1.177 | 0.000277 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 21 | 21 | B.1.177.8 | 0.015801 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 21 | 21 | B.1.620 | 0.019868 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 17 | 17 | B.1.177.32 | 0.022942 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 17 | 17 | P.1.14 | 0.000813 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 12 | 12 | AY.33 | 0.000801 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 11 | 11 | AY.61 | 0.001153 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 11 | 11 | B.1.1.28 | 0.003424 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 11 | 11 | B.1.201 | 0.0625 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 10 | 10 | A.2.5.1 | 0.048077 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 10 | 10 | AY.3 | 0.000099 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 10 | 10 | AY.43 | 0.000044 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 10 | 10 | B.1.1.519 | 0.000397 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 9 | 9 | AY.9.1 | 0.000754 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 9 | 9 | B.1.160 | 0.000281 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 9 | 9 | B.1.160.16 | 0.008364 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 8 | 8 | B.1.177.35 | 0.005529 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 7 | 7 | B.1.405 | 0.08642 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 6 | 6 | AY.11 | 0.008032 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 6 | 6 | B.1.1.216 | 0.005343 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 6 | 6 | B.1.1.432 | 0.007595 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 6 | 6 | B.1.36 | 0.000875 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 6 | 6 | B.1.369 | 0.001711 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 6 | 6 | Q.1 | 0.000758 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | AY.121 | 0.000677 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | AY.26 | 0.000142 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | B.1.1.284 | 0.000537 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | B.1.1.34 | 0.065789 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | B.1.258 | 0.000333 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | B.1.351 | 0.000149 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | B.1.596 | 0.000436 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | C.16 | 0.005302 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | P.1.15 | 0.001162 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 5 | 5 | Q.8 | 0.000825 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 4 | 0.166667 | |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | AY.102 | 0.000106 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | AY.14 | 0.000352 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | AY.2 | 0.001425 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | AY.9.2 | 0.000147 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | AY.98 | 0.000316 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | B | 0.000511 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | B.1.177.17 | 0.003284 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 4 | 4 | P.1.17 | 0.000647 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | AY.23 | 0.000209 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | AY.35 | 0.000699 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | B.1.229 | 0.029126 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | B.1.234 | 0.000396 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | B.1.409 | 0.002344 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | B.1.429 | 0.000071 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | B.1.525 | 0.000339 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 3 | 3 | P.1.12 | 0.001452 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | AY.119 | 0.000071 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | AY.3.1 | 0.000171 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | AY.48 | 0.00093 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | AY.54 | 0.000191 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | AY.67 | 0.000929 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | AY.75.1 | 0.000361 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.220 | 0.003717 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.285 | 0.013072 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.316 | 0.00185 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.372 | 0.001377 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.39 | 0.001019 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.392 | 0.105263 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.448 | 0.004065 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.1.70 | 0.000682 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.139 | 0.001466 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.239 | 0.002442 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.243.2 | 0.028986 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.337 | 0.011173 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.362 | 0.003082 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.375 | 0.001639 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.438.1 | 0.000215 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | B.1.619.1 | 0.001283 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 2 | 2 | P.2 | 0.000373 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | A | 0.000387 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | A.2.2 | 0.001689 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | A.27 | 0.001656 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.10 | 0.00053 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.16.1 | 0.00047 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.19 | 0.00114 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.41 | 0.000294 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.64 | 0.000595 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.78 | 0.001541 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.101 | 0.01 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.110 | 0.090909 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.111 | 0.014706 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.132 | 0.014925 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.257 | 0.009709 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.279 | 0.001121 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.312 | 0.001912 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.317 | 0.000412 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.413 | 0.006897 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.50 | 0.000679 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.518 | 0.006329 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.525 | 0.005464 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.1.63 | 0.000386 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.157 | 0.002985 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.169 | 0.014925 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.177.16 | 0.000664 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.177.5 | 0.001242 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.177.6 | 0.000977 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.214.2 | 0.0006 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.241 | 0.000812 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.258.7 | 0.001912 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.298 | 0.002114 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.320 | 0.001245 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.36.7 | 0.004 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.377 | 0.004566 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.401 | 0.008197 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.425 | 0.002994 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.428.2 | 0.033333 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.509 | 0.000866 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.517 | 0.000427 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.558 | 0.004566 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.576 | 0.000907 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.636 | 0.006711 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.1.94 | 0.027027 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | B.47 | 0.020408 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | C.4 | 0.01 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | C.6 | 0.037037 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp5A-B | 96 | P96L | cCt | cTt | 1 | 1 | P.1.1 | 0.000318 |
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
|