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 |
N | 3 | D3Y | nonsyn | Gat | Tat | 4416 | 4414 | 0.999547 | 28280-28282 |
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 |
N | 3 | D3Y | Gat | Tat | 4414 | 4416 | All | 0.000844 |
N | 3 | D3Y | Gat | Tat | 1015 | 1015 | B.1.617.1 | 0.1309 |
N | 3 | D3Y | Gat | Tat | 498 | 498 | B.1.429 | 0.011717 |
N | 3 | D3Y | Gat | Tat | 297 | 297 | B.1.1.306 | 0.130206 |
N | 3 | D3Y | Gat | Tat | 263 | 263 | B.1 | 0.002409 |
N | 3 | D3Y | Gat | Tat | 221 | 222 | B.1.160 | 0.006892 |
N | 3 | D3Y | Gat | Tat | 184 | 184 | B.1.1.204 | 0.559271 |
N | 3 | D3Y | Gat | Tat | 174 | 174 | B.1.626 | 0.994286 |
N | 3 | D3Y | Gat | Tat | 173 | 173 | B.1.258 | 0.011513 |
N | 3 | D3Y | Gat | Tat | 153 | 153 | AY.4 | 0.000238 |
N | 3 | D3Y | Gat | Tat | 132 | 132 | B.1.1 | 0.002395 |
N | 3 | D3Y | Gat | Tat | 131 | 131 | B.1.369 | 0.037365 |
N | 3 | D3Y | Gat | Tat | 98 | 98 | B.1.36 | 0.014298 |
N | 3 | D3Y | Gat | Tat | 58 | 58 | B.1.1.70 | 0.019782 |
N | 3 | D3Y | Gat | Tat | 58 | 58 | B.1.471 | 0.15847 |
N | 3 | D3Y | Gat | Tat | 56 | 56 | C.31 | 1 |
N | 3 | D3Y | Gat | Tat | 54 | 54 | B.1.397 | 0.262136 |
N | 3 | D3Y | Gat | Tat | 46 | 46 | B.1.460 | 0.821429 |
N | 3 | D3Y | Gat | Tat | 35 | 35 | AY.14 | 0.00308 |
N | 3 | D3Y | Gat | Tat | 35 | 35 | B.1.538 | 0.282258 |
N | 3 | D3Y | Gat | Tat | 34 | 34 | B.1.617.2 | 0.000128 |
N | 3 | D3Y | Gat | Tat | 31 | 31 | P.1 | 0.000488 |
N | 3 | D3Y | Gat | Tat | 30 | 30 | AM.3 | 1 |
N | 3 | D3Y | Gat | Tat | 29 | 29 | B.1.609 | 0.013902 |
N | 3 | D3Y | Gat | Tat | 28 | 28 | B.1.525 | 0.003168 |
N | 3 | D3Y | Gat | Tat | 27 | 27 | B.1.478 | 0.317647 |
N | 3 | D3Y | Gat | Tat | 23 | 23 | B.1.1.216 | 0.020481 |
N | 3 | D3Y | Gat | Tat | 23 | 23 | B.1.422 | 0.018684 |
N | 3 | D3Y | Gat | Tat | 20 | 20 | B.1.177 | 0.000263 |
N | 3 | D3Y | Gat | Tat | 20 | 20 | B.1.565 | 0.016207 |
N | 3 | D3Y | Gat | Tat | 19 | 19 | B.1.1.434 | 0.006623 |
N | 3 | D3Y | Gat | Tat | 18 | 18 | AY.75 | 0.001008 |
N | 3 | D3Y | Gat | Tat | 18 | 18 | B.1.1.1 | 0.00588 |
N | 3 | D3Y | Gat | Tat | 15 | 15 | B.1.177.16 | 0.009967 |
N | 3 | D3Y | Gat | Tat | 15 | 15 | B.1.427 | 0.000757 |
N | 3 | D3Y | Gat | Tat | 14 | 14 | B.1.2 | 0.000123 |
N | 3 | D3Y | Gat | Tat | 13 | 13 | AY.29 | 0.000205 |
N | 3 | D3Y | Gat | Tat | 12 | 12 | AY.47 | 0.000373 |
N | 3 | D3Y | Gat | Tat | 11 | 11 | AY.44 | 0.000067 |
N | 3 | D3Y | Gat | Tat | 10 | 11 | B.1.1.7 | 0.000009 |
N | 3 | D3Y | Gat | Tat | 11 | 11 | B.1.9.5 | 0.0625 |
N | 3 | D3Y | Gat | Tat | 10 | 10 | B.1.1.50 | 0.006789 |
N | 3 | D3Y | Gat | Tat | 10 | 10 | B.1.1.519 | 0.000397 |
N | 3 | D3Y | Gat | Tat | 10 | 10 | B.1.160.8 | 0.012887 |
N | 3 | D3Y | Gat | Tat | 10 | 10 | B.1.526 | 0.000235 |
N | 3 | D3Y | Gat | Tat | 7 | 7 | AY.118 | 0.000439 |
N | 3 | D3Y | Gat | Tat | 7 | 7 | AY.43 | 0.000031 |
N | 3 | D3Y | Gat | Tat | 7 | 7 | AY.61 | 0.000733 |
N | 3 | D3Y | Gat | Tat | 6 | 6 | B.1.1.222 | 0.001224 |
N | 3 | D3Y | Gat | Tat | 6 | 6 | B.1.1.25 | 0.003411 |
N | 3 | D3Y | Gat | Tat | 6 | 6 | B.1.540 | 0.058252 |
N | 3 | D3Y | Gat | Tat | 6 | 6 | P.1.12 | 0.002904 |
N | 3 | D3Y | Gat | Tat | 5 | 5 | B.1.356 | 0.008636 |
N | 3 | D3Y | Gat | Tat | 5 | 5 | B.1.36.22 | 0.006039 |
N | 3 | D3Y | Gat | Tat | 5 | 5 | B.1.367 | 0.003962 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | AD.2 | 0.000876 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | AU.2 | 0.009685 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | AY.102 | 0.000106 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | AY.25 | 0.000024 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | AY.26 | 0.000113 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | AY.39 | 0.000099 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | AY.9 | 0.00027 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | B | 0.000511 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | B.1.177.73 | 0.002265 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | B.1.177.85 | 0.021739 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | B.1.258.14 | 0.003922 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | B.1.466.2 | 0.001565 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | B.1.596 | 0.000349 |
N | 3 | D3Y | Gat | Tat | 4 | 4 | P.1.17 | 0.000647 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | AY.3 | 0.00003 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | AY.6 | 0.000123 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | AY.74 | 0.000347 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.1.171 | 0.011029 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.1.28 | 0.000934 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.1.294 | 0.003797 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.243 | 0.000209 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.36.8 | 0.003 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.560 | 0.013889 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.564 | 0.001278 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.619 | 0.002613 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | B.1.637 | 0.000219 |
N | 3 | D3Y | Gat | Tat | 3 | 3 | C.35 | 0.002322 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | A | 0.000774 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | A.19 | 0.018868 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AE.6 | 0.076923 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AM.4 | 0.007143 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AY.10 | 0.00106 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AY.100 | 0.000092 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AY.103 | 0.000012 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AY.27 | 0.000129 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AY.46.4 | 0.000329 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | AY.54 | 0.000191 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.1.348 | 0.001592 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.1.409 | 0.005666 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.177.86 | 0.000367 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.221 | 0.000142 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.258.17 | 0.000208 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.351 | 0.000059 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.620 | 0.001892 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | B.1.621 | 0.000177 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | C.16 | 0.002121 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | C.26 | 0.014706 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | C.36 | 0.001821 |
N | 3 | D3Y | Gat | Tat | 2 | 2 | C.6 | 0.074074 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | 0.055556 | |
N | 3 | D3Y | Gat | Tat | 1 | 1 | A.1 | 0.000282 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | A.18 | 0.05 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | A.3 | 0.002096 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AE.4 | 0.043478 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.107 | 0.000466 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.109 | 0.00074 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.120 | 0.000037 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.13 | 0.000161 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.16.1 | 0.00047 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.20 | 0.000039 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.34.1 | 0.00051 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.35 | 0.000233 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.42 | 0.00004 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.45 | 0.000122 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.46.6 | 0.000072 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.55 | 0.000917 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.66 | 0.00107 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.75.1 | 0.00018 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.85 | 0.000427 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.91 | 0.00073 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | AY.98 | 0.000079 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.10 | 0.001115 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.109 | 0.04 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.133 | 0.008475 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.145 | 0.037037 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.194 | 0.00495 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.198 | 0.001468 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.214 | 0.000055 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.237 | 0.005405 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.277 | 0.000759 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.284 | 0.000107 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.307 | 0.002532 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.316 | 0.000925 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.318 | 0.000302 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.322 | 0.008772 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.354 | 0.004386 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.359 | 0.027778 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.375 | 0.011905 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.448 | 0.002033 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.526 | 0.003546 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.1.54 | 0.003021 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.111 | 0.001175 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.140 | 0.018868 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.177.81 | 0.000189 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.214 | 0.003663 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.222 | 0.001692 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.234 | 0.000132 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.258.11 | 0.000396 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.320 | 0.001245 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.36.10 | 0.004785 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.400 | 0.000429 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.428 | 0.00102 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.432 | 0.011236 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.456 | 0.003268 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.480 | 0.002488 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.509 | 0.000866 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.524 | 0.001406 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.533 | 0.009615 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.541 | 0.004425 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.549 | 0.007194 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.558 | 0.004566 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.568 | 0.001111 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.595 | 0.000261 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.601 | 0.030303 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.612 | 0.002653 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.623 | 0.000536 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.1.628 | 0.000352 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | B.40 | 0.000364 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | C.37 | 0.000116 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | D.2 | 0.000075 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | N.5 | 0.001767 |
N | 3 | D3Y | Gat | Tat | 1 | 1 | P.1.10 | 0.000269 |
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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