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 |
noncoding | 28269 | C28269T | noncoding | C | T | 2462 | 2462 | 1 | 28269-28269 | |
noncoding | 28269 | C28269A | noncoding | C | A | 1021 | 1021 | 1 | 28269-28269 | |
noncoding | 28269 | C28269- | noncoding | C | - | 258 | 258 | 1 | 28269-28269 | |
noncoding | 28269 | C28269G | noncoding | C | G | 4 | 4 | 1 | 28269-28269 |
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 |
noncoding | 28269 | C28269T | C | T | 2462 | 2462 | All | 0.000471 |
noncoding | 28269 | C28269T | C | T | 1654 | 1654 | B.1.1.7 | 0.001481 |
noncoding | 28269 | C28269A | C | A | 1021 | 1021 | All | 0.000195 |
noncoding | 28269 | C28269- | C | - | 258 | 258 | All | 0.000049 |
noncoding | 28269 | C28269T | C | T | 228 | 228 | B.1.149 | 0.780822 |
noncoding | 28269 | C28269- | C | - | 219 | 219 | AY.34 | 0.021235 |
noncoding | 28269 | C28269A | C | A | 166 | 166 | B.1.617.1 | 0.021408 |
noncoding | 28269 | C28269A | C | A | 99 | 99 | P.1 | 0.00156 |
noncoding | 28269 | C28269A | C | A | 86 | 86 | B.1.617.2 | 0.000324 |
noncoding | 28269 | C28269T | C | T | 82 | 82 | AY.103 | 0.000509 |
noncoding | 28269 | C28269A | C | A | 82 | 82 | AY.4 | 0.000128 |
noncoding | 28269 | C28269A | C | A | 70 | 70 | B.1.1.7 | 0.000063 |
noncoding | 28269 | C28269A | C | A | 52 | 52 | AY.43 | 0.00023 |
noncoding | 28269 | C28269T | C | T | 49 | 49 | B.1.2 | 0.000431 |
noncoding | 28269 | C28269T | C | T | 44 | 44 | B.1.509 | 0.038095 |
noncoding | 28269 | C28269T | C | T | 43 | 43 | B.1.177 | 0.000566 |
noncoding | 28269 | C28269A | C | A | 39 | 39 | AY.98.1 | 0.001889 |
noncoding | 28269 | C28269A | C | A | 38 | 38 | AY.44 | 0.000231 |
noncoding | 28269 | C28269T | C | T | 37 | 37 | B.1 | 0.000339 |
noncoding | 28269 | C28269T | C | T | 35 | 35 | AY.4 | 0.000054 |
noncoding | 28269 | C28269T | C | T | 32 | 32 | B.1.617.1 | 0.004127 |
noncoding | 28269 | C28269A | C | A | 25 | 25 | AY.23 | 0.001744 |
noncoding | 28269 | C28269T | C | T | 25 | 25 | B.1.1 | 0.000454 |
noncoding | 28269 | C28269A | C | A | 24 | 24 | P.1.12 | 0.011617 |
noncoding | 28269 | C28269A | C | A | 22 | 22 | AY.103 | 0.000137 |
noncoding | 28269 | C28269A | C | A | 21 | 21 | P.1.17 | 0.003397 |
noncoding | 28269 | C28269A | C | A | 19 | 19 | B.1 | 0.000174 |
noncoding | 28269 | C28269A | C | A | 17 | 17 | AY.102 | 0.000451 |
noncoding | 28269 | C28269A | C | A | 17 | 17 | AY.16 | 0.006454 |
noncoding | 28269 | C28269T | C | T | 17 | 17 | AY.44 | 0.000103 |
noncoding | 28269 | C28269A | C | A | 17 | 17 | AY.61 | 0.001781 |
noncoding | 28269 | C28269T | C | T | 17 | 17 | B.1.177.21 | 0.0013 |
noncoding | 28269 | C28269T | C | T | 16 | 16 | AY.29 | 0.000252 |
noncoding | 28269 | C28269A | C | A | 16 | 16 | B.1.1.28 | 0.00498 |
noncoding | 28269 | C28269T | C | T | 15 | 15 | B.1.617.2 | 0.000056 |
noncoding | 28269 | C28269A | C | A | 14 | 14 | AY.113 | 0.001993 |
noncoding | 28269 | C28269T | C | T | 11 | 11 | AY.25 | 0.000066 |
noncoding | 28269 | C28269A | C | A | 11 | 11 | AY.68 | 0.003011 |
noncoding | 28269 | C28269- | C | - | 11 | 11 | B.1.1.7 | 0.00001 |
noncoding | 28269 | C28269A | C | A | 11 | 11 | B.1.617.3 | 0.032836 |
noncoding | 28269 | C28269A | C | A | 10 | 10 | AY.119 | 0.000353 |
noncoding | 28269 | C28269T | C | T | 10 | 10 | B.1.351 | 0.000297 |
noncoding | 28269 | C28269- | C | - | 10 | 10 | B.1.617.2 | 0.000038 |
noncoding | 28269 | C28269T | C | T | 9 | 9 | B.1.1.523 | 0.014063 |
noncoding | 28269 | C28269A | C | A | 8 | 8 | AY.29 | 0.000126 |
noncoding | 28269 | C28269A | C | A | 7 | 7 | AY.45 | 0.000852 |
noncoding | 28269 | C28269A | C | A | 7 | 7 | AY.55 | 0.006422 |
noncoding | 28269 | C28269A | C | A | 7 | 7 | AY.95 | 0.005327 |
noncoding | 28269 | C28269A | C | A | 7 | 7 | B.1.1 | 0.000127 |
noncoding | 28269 | C28269T | C | T | 7 | 7 | B.1.1.519 | 0.000278 |
noncoding | 28269 | C28269A | C | A | 7 | 7 | B.1.177.15 | 0.004416 |
noncoding | 28269 | C28269T | C | T | 7 | 7 | B.55 | 0.020649 |
noncoding | 28269 | C28269A | C | A | 7 | 7 | P.1.10 | 0.001886 |
noncoding | 28269 | C28269A | C | A | 6 | 6 | AY.16.1 | 0.00282 |
noncoding | 28269 | C28269A | C | A | 6 | 6 | AY.26 | 0.00017 |
noncoding | 28269 | C28269A | C | A | 6 | 6 | AY.32 | 0.003195 |
noncoding | 28269 | C28269A | C | A | 6 | 6 | AY.40 | 0.005786 |
noncoding | 28269 | C28269T | C | T | 6 | 6 | B.1.36.29 | 0.003104 |
noncoding | 28269 | C28269T | C | T | 5 | 5 | AY.3 | 0.00005 |
noncoding | 28269 | C28269T | C | T | 5 | 5 | AY.43 | 0.000022 |
noncoding | 28269 | C28269A | C | A | 5 | 5 | AY.92 | 0.001436 |
noncoding | 28269 | C28269- | C | - | 5 | 5 | B.1.149 | 0.017123 |
noncoding | 28269 | C28269G | C | G | 4 | 4 | All | 0.000001 |
noncoding | 28269 | C28269A | C | A | 4 | 4 | AY.100 | 0.000184 |
noncoding | 28269 | C28269A | C | A | 4 | 4 | AY.118 | 0.000251 |
noncoding | 28269 | C28269A | C | A | 4 | 4 | AY.20 | 0.000155 |
noncoding | 28269 | C28269T | C | T | 4 | 4 | AY.46 | 0.000416 |
noncoding | 28269 | C28269T | C | T | 4 | 4 | B.1.1.198 | 0.005874 |
noncoding | 28269 | C28269T | C | T | 4 | 4 | B.1.258.17 | 0.000416 |
noncoding | 28269 | C28269T | C | T | 4 | 4 | B.1.429 | 0.000094 |
noncoding | 28269 | C28269A | C | A | 4 | 4 | B.1.438.1 | 0.000429 |
noncoding | 28269 | C28269T | C | T | 3 | 3 | AY.100 | 0.000138 |
noncoding | 28269 | C28269A | C | A | 3 | 3 | AY.116 | 0.00086 |
noncoding | 28269 | C28269T | C | T | 3 | 3 | AY.13 | 0.000483 |
noncoding | 28269 | C28269A | C | A | 3 | 3 | AY.25 | 0.000018 |
noncoding | 28269 | C28269A | C | A | 3 | 3 | AY.75 | 0.000168 |
noncoding | 28269 | C28269A | C | A | 3 | 3 | AY.9.2 | 0.00011 |
noncoding | 28269 | C28269T | C | T | 3 | 3 | B.1.1.525 | 0.016393 |
noncoding | 28269 | C28269A | C | A | 3 | 3 | B.1.2 | 0.000026 |
noncoding | 28269 | C28269T | C | T | 3 | 3 | B.1.258 | 0.0002 |
noncoding | 28269 | C28269T | C | T | 3 | 3 | B.1.596 | 0.000261 |
noncoding | 28269 | C28269T | C | T | 3 | 3 | C.35 | 0.002322 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.101 | 0.000981 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.107 | 0.000932 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | AY.110 | 0.000225 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.117 | 0.000169 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.121 | 0.000271 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | AY.14 | 0.000176 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | AY.26 | 0.000057 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.3 | 0.00002 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.38 | 0.000999 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | AY.4.2 | 0.000043 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.42 | 0.00008 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.46 | 0.000208 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.46.6 | 0.000144 |
noncoding | 28269 | C28269- | C | - | 2 | 2 | AY.47 | 0.000062 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | AY.75.1 | 0.000361 |
noncoding | 28269 | C28269- | C | - | 2 | 2 | AY.75.1 | 0.000361 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | AY.99.2 | 0.000184 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | B.1.160 | 0.000062 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | B.1.162 | 0.01005 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | B.1.214 | 0.007326 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | B.1.36.17 | 0.000988 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | B.1.367 | 0.001585 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | B.1.399 | 0.003868 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | B.1.525 | 0.000226 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | B.1.575 | 0.000607 |
noncoding | 28269 | C28269T | C | T | 2 | 2 | P.1 | 0.000032 |
noncoding | 28269 | C28269A | C | A | 2 | 2 | P.1.13 | 0.001797 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | 0.055556 | |
noncoding | 28269 | C28269T | C | T | 1 | 1 | A | 0.000387 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | A.2 | 0.000662 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.1 | 0.000396 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.1 | 0.000396 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.106 | 0.000335 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.109 | 0.00074 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | AY.110 | 0.000113 |
noncoding | 28269 | C28269G | C | G | 1 | 1 | AY.113 | 0.000142 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | AY.119 | 0.000035 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.12 | 0.000316 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | AY.120 | 0.000037 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.120 | 0.000037 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.13 | 0.000161 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.16 | 0.00038 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.19 | 0.00114 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.21 | 0.001898 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | AY.33 | 0.000067 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.36 | 0.000148 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.39 | 0.000025 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | AY.4 | 0.000002 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.4.2 | 0.000022 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.4.2.1 | 0.000149 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.4.4 | 0.000409 |
noncoding | 28269 | C28269G | C | G | 1 | 1 | AY.43 | 0.000004 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.48 | 0.000465 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.5 | 0.000021 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.50 | 0.000799 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.52 | 0.000814 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.53 | 0.000288 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.54 | 0.000095 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.64 | 0.000595 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.70 | 0.000209 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.71 | 0.000475 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.74 | 0.000116 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.77 | 0.001127 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.78 | 0.001541 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.80 | 0.001129 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.84 | 0.000437 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.87 | 0.000833 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | AY.91 | 0.00073 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.98 | 0.000079 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.98.1 | 0.000048 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | AY.99 | 0.001049 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | B.1.1 | 0.000018 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.174 | 0.003378 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.176 | 0.000439 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.214 | 0.000055 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | B.1.1.222 | 0.000204 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.222 | 0.000204 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.231 | 0.003096 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.284 | 0.000107 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | B.1.1.311 | 0.000358 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.316 | 0.000925 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.37 | 0.000193 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.376 | 0.005952 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.39 | 0.00051 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | B.1.1.63 | 0.000386 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.1.70 | 0.000341 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.177.55 | 0.002331 |
noncoding | 28269 | C28269G | C | G | 1 | 1 | B.1.177.63 | 0.002703 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.177.83 | 0.001481 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | B.1.210 | 0.002132 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.232 | 0.000537 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.239 | 0.001221 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.243 | 0.00007 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.265 | 0.001271 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.305 | 0.002151 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.349 | 0.000715 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.36 | 0.000146 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.36.1 | 0.00114 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | B.1.36.18 | 0.00042 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.39 | 0.003906 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | B.1.39 | 0.003906 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.503 | 0.002488 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | B.1.526 | 0.000024 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.548 | 0.035714 |
noncoding | 28269 | C28269G | C | G | 1 | 1 | B.1.558 | 0.004566 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | B.1.596 | 0.000087 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.617.3 | 0.002985 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.621 | 0.000089 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.637 | 0.000073 |
noncoding | 28269 | C28269- | C | - | 1 | 1 | B.1.637 | 0.000073 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | B.1.77 | 0.045455 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | C.16 | 0.00106 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | D.2 | 0.000075 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | D.2 | 0.000075 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | P.1.14 | 0.000048 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | P.2 | 0.000187 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | Q.1 | 0.000126 |
noncoding | 28269 | C28269T | C | T | 1 | 1 | Q.8 | 0.000165 |
noncoding | 28269 | C28269A | C | A | 1 | 1 | Q.8 | 0.000165 |
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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