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 | 256 | S256L | nonsyn | tCa | tTa | 4580 | 4580 | 1 | 22328-22330 |
Details of the mutation S256L 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 | 256 | S256L | tCa | tTa | 4580 | 4580 | All | 0.000876 |
S | 256 | S256L | tCa | tTa | 999 | 999 | B.1.177 | 0.013154 |
S | 256 | S256L | tCa | tTa | 896 | 896 | AY.4 | 0.001395 |
S | 256 | S256L | tCa | tTa | 578 | 578 | B.1.1.7 | 0.000517 |
S | 256 | S256L | tCa | tTa | 317 | 317 | B.1.1.214 | 0.01758 |
S | 256 | S256L | tCa | tTa | 218 | 218 | B.1.369 | 0.062179 |
S | 256 | S256L | tCa | tTa | 162 | 162 | B.1.177.7 | 0.026706 |
S | 256 | S256L | tCa | tTa | 96 | 96 | B.1.617.2 | 0.000361 |
S | 256 | S256L | tCa | tTa | 94 | 94 | B.1.2 | 0.000828 |
S | 256 | S256L | tCa | tTa | 69 | 69 | AY.43 | 0.000306 |
S | 256 | S256L | tCa | tTa | 68 | 68 | AY.44 | 0.000414 |
S | 256 | S256L | tCa | tTa | 63 | 63 | B.1.429 | 0.001482 |
S | 256 | S256L | tCa | tTa | 60 | 60 | AY.103 | 0.000373 |
S | 256 | S256L | tCa | tTa | 56 | 56 | B.1.177.39 | 0.861538 |
S | 256 | S256L | tCa | tTa | 55 | 55 | AY.25 | 0.000331 |
S | 256 | S256L | tCa | tTa | 50 | 50 | B.1.526 | 0.001175 |
S | 256 | S256L | tCa | tTa | 44 | 44 | AY.90 | 0.030116 |
S | 256 | S256L | tCa | tTa | 40 | 40 | AY.14 | 0.003521 |
S | 256 | S256L | tCa | tTa | 37 | 37 | B.1 | 0.000339 |
S | 256 | S256L | tCa | tTa | 31 | 31 | B.1.1 | 0.000562 |
S | 256 | S256L | tCa | tTa | 28 | 28 | B.1.177.47 | 0.363636 |
S | 256 | S256L | tCa | tTa | 21 | 21 | AY.3 | 0.000209 |
S | 256 | S256L | tCa | tTa | 21 | 21 | B.1.1.222 | 0.004284 |
S | 256 | S256L | tCa | tTa | 18 | 18 | B.1.577 | 0.012371 |
S | 256 | S256L | tCa | tTa | 18 | 18 | P.1 | 0.000284 |
S | 256 | S256L | tCa | tTa | 16 | 16 | AY.92 | 0.004596 |
S | 256 | S256L | tCa | tTa | 14 | 14 | AY.13 | 0.002254 |
S | 256 | S256L | tCa | tTa | 13 | 13 | AY.23 | 0.000907 |
S | 256 | S256L | tCa | tTa | 13 | 13 | AY.4.2 | 0.000282 |
S | 256 | S256L | tCa | tTa | 13 | 13 | AY.75 | 0.000728 |
S | 256 | S256L | tCa | tTa | 13 | 13 | AY.9 | 0.000879 |
S | 256 | S256L | tCa | tTa | 12 | 12 | AY.119 | 0.000424 |
S | 256 | S256L | tCa | tTa | 11 | 11 | AY.39 | 0.000272 |
S | 256 | S256L | tCa | tTa | 11 | 11 | AY.74 | 0.001272 |
S | 256 | S256L | tCa | tTa | 11 | 11 | B.1.221 | 0.000781 |
S | 256 | S256L | tCa | tTa | 11 | 11 | C.37 | 0.001277 |
S | 256 | S256L | tCa | tTa | 10 | 10 | AY.33 | 0.000668 |
S | 256 | S256L | tCa | tTa | 10 | 10 | B.1.427 | 0.000505 |
S | 256 | S256L | tCa | tTa | 9 | 9 | B.1.1.519 | 0.000357 |
S | 256 | S256L | tCa | tTa | 9 | 9 | D.2 | 0.000675 |
S | 256 | S256L | tCa | tTa | 9 | 9 | Q.8 | 0.001484 |
S | 256 | S256L | tCa | tTa | 8 | 8 | AY.120 | 0.000297 |
S | 256 | S256L | tCa | tTa | 8 | 8 | AY.29 | 0.000126 |
S | 256 | S256L | tCa | tTa | 8 | 8 | AY.32 | 0.00426 |
S | 256 | S256L | tCa | tTa | 8 | 8 | AY.42 | 0.000322 |
S | 256 | S256L | tCa | tTa | 8 | 8 | B.1.1.318 | 0.002414 |
S | 256 | S256L | tCa | tTa | 8 | 8 | B.1.311 | 0.002197 |
S | 256 | S256L | tCa | tTa | 8 | 8 | B.1.351 | 0.000238 |
S | 256 | S256L | tCa | tTa | 8 | 8 | B.1.36.21 | 0.017279 |
S | 256 | S256L | tCa | tTa | 7 | 7 | AY.120.1 | 0.002247 |
S | 256 | S256L | tCa | tTa | 7 | 7 | AY.46 | 0.000729 |
S | 256 | S256L | tCa | tTa | 7 | 7 | B.1.258 | 0.000466 |
S | 256 | S256L | tCa | tTa | 6 | 6 | AY.26 | 0.00017 |
S | 256 | S256L | tCa | tTa | 6 | 6 | AY.54 | 0.000572 |
S | 256 | S256L | tCa | tTa | 6 | 6 | AY.98 | 0.000474 |
S | 256 | S256L | tCa | tTa | 6 | 6 | B.1.177.79 | 0.014052 |
S | 256 | S256L | tCa | tTa | 6 | 6 | B.1.177.81 | 0.001136 |
S | 256 | S256L | tCa | tTa | 5 | 5 | AY.100 | 0.00023 |
S | 256 | S256L | tCa | tTa | 5 | 5 | AY.3.1 | 0.000426 |
S | 256 | S256L | tCa | tTa | 5 | 5 | AY.5 | 0.000103 |
S | 256 | S256L | tCa | tTa | 5 | 5 | B.1.1.311 | 0.001791 |
S | 256 | S256L | tCa | tTa | 5 | 5 | B.1.367 | 0.003962 |
S | 256 | S256L | tCa | tTa | 5 | 5 | B.1.525 | 0.000566 |
S | 256 | S256L | tCa | tTa | 5 | 5 | R.1 | 0.00045 |
S | 256 | S256L | tCa | tTa | 4 | 4 | AY.20 | 0.000155 |
S | 256 | S256L | tCa | tTa | 4 | 4 | AY.6 | 0.000165 |
S | 256 | S256L | tCa | tTa | 4 | 4 | B.1.1.159 | 0.018692 |
S | 256 | S256L | tCa | tTa | 4 | 4 | B.1.1.306 | 0.001754 |
S | 256 | S256L | tCa | tTa | 4 | 4 | B.1.177.12 | 0.000607 |
S | 256 | S256L | tCa | tTa | 4 | 4 | B.1.214.2 | 0.002398 |
S | 256 | S256L | tCa | tTa | 4 | 4 | B.1.561 | 0.001588 |
S | 256 | S256L | tCa | tTa | 4 | 4 | Q.3 | 0.00058 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.111 | 0.000549 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.16 | 0.001139 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.24 | 0.001293 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.36 | 0.000445 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.45 | 0.000365 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.55 | 0.002752 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.61 | 0.000314 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.71 | 0.001425 |
S | 256 | S256L | tCa | tTa | 3 | 3 | AY.9.2 | 0.00011 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.1.176 | 0.001318 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.1.70 | 0.001023 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.131 | 0.026316 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.160 | 0.000094 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.243 | 0.000209 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.258.17 | 0.000312 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.408 | 0.01107 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.617.1 | 0.000387 |
S | 256 | S256L | tCa | tTa | 3 | 3 | B.1.625 | 0.007059 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.102 | 0.000053 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.113 | 0.000285 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.117 | 0.000169 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.118 | 0.000125 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.39.1 | 0.000079 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.39.2 | 0.003082 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.47 | 0.000062 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.7 | 0.000392 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.9.1 | 0.000167 |
S | 256 | S256L | tCa | tTa | 2 | 2 | AY.99.2 | 0.000184 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.1.166 | 0.066667 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.1.216 | 0.001781 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.1.416 | 0.00181 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.177.21 | 0.000153 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.177.77 | 0.001452 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.177.87 | 0.001456 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.234 | 0.000264 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.239 | 0.002442 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.240 | 0.000431 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.36 | 0.000292 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.409 | 0.001563 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.438.1 | 0.000215 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.466.2 | 0.000782 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.582 | 0.000981 |
S | 256 | S256L | tCa | tTa | 2 | 2 | B.1.595 | 0.000522 |
S | 256 | S256L | tCa | tTa | 2 | 2 | P.2 | 0.000373 |
S | 256 | S256L | tCa | tTa | 2 | 2 | Q.1 | 0.000253 |
S | 256 | S256L | tCa | tTa | 2 | 2 | W.3 | 0.010526 |
S | 256 | S256L | tCa | tTa | 1 | 1 | A.2.5 | 0.000499 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AU.2 | 0.002421 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AW.1 | 0.003049 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.109 | 0.00074 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.110 | 0.000113 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.114 | 0.000231 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.116 | 0.000287 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.116.1 | 0.000311 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.12 | 0.000316 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.121 | 0.000135 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.22 | 0.002092 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.29.1 | 0.000221 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.4.2.1 | 0.000149 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.4.5 | 0.000107 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.5.4 | 0.000277 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.50 | 0.000799 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.73 | 0.000665 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.75.1 | 0.00018 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.84 | 0.000437 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.86 | 0.00083 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.87 | 0.000833 |
S | 256 | S256L | tCa | tTa | 1 | 1 | AY.98.1 | 0.000048 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.101 | 0.01 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.133 | 0.008475 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.198 | 0.001468 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.25 | 0.000569 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.284 | 0.000107 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.317 | 0.000412 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.33 | 0.000421 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.37 | 0.000193 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.372 | 0.000689 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.39 | 0.00051 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.393 | 0.111111 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.432 | 0.001266 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.1.487 | 0.005587 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.124 | 0.007812 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.160.30 | 0.002976 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.177.15 | 0.000631 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.177.16 | 0.000664 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.177.86 | 0.000183 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.236 | 0.002053 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.323 | 0.020833 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.349 | 0.000715 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.36.1 | 0.00114 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.36.28 | 0.005747 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.36.38 | 0.001642 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.439 | 0.005917 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.453 | 0.003236 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.470 | 0.001404 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.497 | 0.000315 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.564 | 0.000426 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.565 | 0.00081 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.575 | 0.000303 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.596 | 0.000087 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.621 | 0.000089 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.1.637 | 0.000073 |
S | 256 | S256L | tCa | tTa | 1 | 1 | B.15 | 0.017544 |
S | 256 | S256L | tCa | tTa | 1 | 1 | P.1.14 | 0.000048 |
S | 256 | S256L | tCa | tTa | 1 | 1 | P.1.2 | 0.001156 |
S | 256 | S256L | tCa | tTa | 1 | 1 | P.1.4 | 0.000977 |
S | 256 | S256L | tCa | tTa | 1 | 1 | P.1.7 | 0.000319 |
S | 256 | S256L | tCa | tTa | 1 | 1 | P.4 | 0.003802 |
S | 256 | S256L | tCa | tTa | 1 | 1 | P.6 | 0.003145 |
S | 256 | S256L | tCa | tTa | 1 | 1 | Q.4 | 0.000455 |
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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