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 | 398 | A398S | nonsyn | Gca | Tca | 1414 | 1412 | 0.998586 | 29465-29467 | |
N | 398 | A398S | nonsyn | GcA | TcC | 1414 | 2 | 0.00141443 | 29465-29467 |
Details of the mutation A398S 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 | 398 | A398S | Gca | Tca | 1412 | 1414 | All | 0.00027 |
N | 398 | A398S | GcA | TcC | 2 | 1414 | All | 0 |
N | 398 | A398S | Gca | Tca | 231 | 232 | AY.4 | 0.00036 |
N | 398 | A398S | GcA | TcC | 1 | 232 | AY.4 | 0.000002 |
N | 398 | A398S | Gca | Tca | 231 | 231 | B.1.617.2 | 0.00087 |
N | 398 | A398S | Gca | Tca | 145 | 145 | AY.98 | 0.011454 |
N | 398 | A398S | Gca | Tca | 125 | 126 | B.1.1.7 | 0.000112 |
N | 398 | A398S | GcA | TcC | 1 | 126 | B.1.1.7 | 0.000001 |
N | 398 | A398S | Gca | Tca | 51 | 51 | AY.43 | 0.000226 |
N | 398 | A398S | Gca | Tca | 46 | 46 | B.1.2 | 0.000405 |
N | 398 | A398S | Gca | Tca | 37 | 37 | AY.103 | 0.00023 |
N | 398 | A398S | Gca | Tca | 24 | 24 | AY.44 | 0.000146 |
N | 398 | A398S | Gca | Tca | 24 | 24 | B.1 | 0.00022 |
N | 398 | A398S | Gca | Tca | 24 | 24 | B.1.177.82 | 0.011456 |
N | 398 | A398S | Gca | Tca | 23 | 23 | AY.20 | 0.000894 |
N | 398 | A398S | Gca | Tca | 21 | 21 | AY.46.6 | 0.001516 |
N | 398 | A398S | Gca | Tca | 19 | 19 | P.1 | 0.000299 |
N | 398 | A398S | Gca | Tca | 18 | 18 | AY.25 | 0.000108 |
N | 398 | A398S | Gca | Tca | 18 | 18 | B.1.396 | 0.012703 |
N | 398 | A398S | Gca | Tca | 16 | 16 | AY.4.2 | 0.000347 |
N | 398 | A398S | Gca | Tca | 15 | 15 | AY.29 | 0.000237 |
N | 398 | A398S | Gca | Tca | 13 | 13 | B.1.177 | 0.000171 |
N | 398 | A398S | Gca | Tca | 12 | 12 | AY.120 | 0.000446 |
N | 398 | A398S | Gca | Tca | 12 | 12 | AY.39 | 0.000297 |
N | 398 | A398S | Gca | Tca | 12 | 12 | B.1.1 | 0.000218 |
N | 398 | A398S | Gca | Tca | 11 | 11 | AY.100 | 0.000506 |
N | 398 | A398S | Gca | Tca | 11 | 11 | AY.39.1 | 0.000436 |
N | 398 | A398S | Gca | Tca | 10 | 10 | AY.75 | 0.00056 |
N | 398 | A398S | Gca | Tca | 10 | 10 | B.1.160 | 0.000312 |
N | 398 | A398S | Gca | Tca | 9 | 9 | AY.3.1 | 0.000767 |
N | 398 | A398S | Gca | Tca | 9 | 9 | P.1.14 | 0.00043 |
N | 398 | A398S | Gca | Tca | 8 | 8 | B.1.1.317 | 0.003294 |
N | 398 | A398S | Gca | Tca | 7 | 7 | AY.102 | 0.000186 |
N | 398 | A398S | Gca | Tca | 7 | 7 | AY.119 | 0.000247 |
N | 398 | A398S | Gca | Tca | 7 | 7 | B.1.526 | 0.000165 |
N | 398 | A398S | Gca | Tca | 6 | 6 | AY.111 | 0.001099 |
N | 398 | A398S | Gca | Tca | 6 | 6 | AY.121 | 0.000812 |
N | 398 | A398S | Gca | Tca | 6 | 6 | AY.34 | 0.000582 |
N | 398 | A398S | Gca | Tca | 6 | 6 | B.1.351 | 0.000178 |
N | 398 | A398S | Gca | Tca | 6 | 6 | B.1.617.1 | 0.000774 |
N | 398 | A398S | Gca | Tca | 5 | 5 | AY.98.1 | 0.000242 |
N | 398 | A398S | Gca | Tca | 5 | 5 | B.1.1.216 | 0.004452 |
N | 398 | A398S | Gca | Tca | 5 | 5 | B.1.1.305 | 0.019305 |
N | 398 | A398S | Gca | Tca | 5 | 5 | B.1.596 | 0.000436 |
N | 398 | A398S | Gca | Tca | 5 | 5 | C.36 | 0.004554 |
N | 398 | A398S | Gca | Tca | 4 | 4 | AY.3 | 0.00004 |
N | 398 | A398S | Gca | Tca | 4 | 4 | AY.46 | 0.000416 |
N | 398 | A398S | Gca | Tca | 4 | 4 | AY.54 | 0.000381 |
N | 398 | A398S | Gca | Tca | 4 | 4 | AY.9.1 | 0.000335 |
N | 398 | A398S | Gca | Tca | 3 | 3 | AY.4.5 | 0.000322 |
N | 398 | A398S | Gca | Tca | 3 | 3 | B.1.1.519 | 0.000119 |
N | 398 | A398S | Gca | Tca | 3 | 3 | B.1.221 | 0.000213 |
N | 398 | A398S | Gca | Tca | 3 | 3 | B.1.36 | 0.000438 |
N | 398 | A398S | Gca | Tca | 3 | 3 | B.1.404 | 0.003906 |
N | 398 | A398S | Gca | Tca | 3 | 3 | B.1.427 | 0.000151 |
N | 398 | A398S | Gca | Tca | 3 | 3 | C.37 | 0.000348 |
N | 398 | A398S | Gca | Tca | 3 | 3 | P.2 | 0.00056 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.113 | 0.000285 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.13 | 0.000322 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.23 | 0.000139 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.26 | 0.000057 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.45 | 0.000243 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.46.3 | 0.001867 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.47 | 0.000062 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.5.3 | 0.000675 |
N | 398 | A398S | Gca | Tca | 2 | 2 | AY.9.2 | 0.000073 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.1.222 | 0.000408 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.1.258 | 0.006515 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.1.306 | 0.000877 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.1.34 | 0.026316 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.1.354 | 0.008772 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.160.17 | 0.003401 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.240 | 0.000431 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.243 | 0.000139 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.429 | 0.000047 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.1.609 | 0.000959 |
N | 398 | A398S | Gca | Tca | 2 | 2 | B.4 | 0.004415 |
N | 398 | A398S | Gca | Tca | 2 | 2 | D.2 | 0.00015 |
N | 398 | A398S | Gca | Tca | 2 | 2 | Q.8 | 0.00033 |
N | 398 | A398S | Gca | Tca | 2 | 2 | R.1 | 0.00018 |
N | 398 | A398S | Gca | Tca | 1 | 1 | A.2.2 | 0.001689 |
N | 398 | A398S | Gca | Tca | 1 | 1 | A.23.1 | 0.000704 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.104 | 0.001984 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.106 | 0.000335 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.107 | 0.000466 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.108 | 0.001103 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.109 | 0.00074 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.116 | 0.000287 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.118 | 0.000063 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.120.2 | 0.001285 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.14 | 0.000088 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.16 | 0.00038 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.29.1 | 0.000221 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.4.4 | 0.000409 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.42 | 0.00004 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.46.1 | 0.001027 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.5 | 0.000021 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.52 | 0.000814 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.55 | 0.000917 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.59 | 0.00053 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.6 | 0.000041 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.62 | 0.000436 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.65 | 0.000533 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.72 | 0.001361 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.74 | 0.000116 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.86 | 0.00083 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.9 | 0.000068 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AY.92 | 0.000287 |
N | 398 | A398S | Gca | Tca | 1 | 1 | AZ.2 | 0.000821 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B | 0.000128 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.141 | 0.002012 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.181 | 0.004545 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.220 | 0.001859 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.326 | 0.001761 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.366 | 0.015873 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.409 | 0.002833 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.416 | 0.000905 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.433 | 0.001425 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.434 | 0.000349 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.51 | 0.001718 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.63 | 0.000386 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.1.83 | 0.00271 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.127 | 0.002198 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.160.8 | 0.001289 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.177.21 | 0.000076 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.177.46 | 0.000918 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.177.5 | 0.001242 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.177.62 | 0.001192 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.234 | 0.000132 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.258 | 0.000067 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.258.17 | 0.000104 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.336 | 0.002439 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.351.2 | 0.000303 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.356 | 0.001727 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.391 | 0.001127 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.402 | 0.009804 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.422 | 0.000812 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.456 | 0.003268 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.488 | 0.2 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.510 | 0.026316 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.575 | 0.000303 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.595 | 0.000261 |
N | 398 | A398S | Gca | Tca | 1 | 1 | B.1.637 | 0.000073 |
N | 398 | A398S | Gca | Tca | 1 | 1 | P.1.12 | 0.000484 |
N | 398 | A398S | Gca | Tca | 1 | 1 | P.7 | 0.004367 |
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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