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 |
ORF3a | 24 | T24I | nonsyn | aCt | aTt | 7405 | 7402 | 0.999595 | 25462-25464 | |
ORF3a | 24 | T24I | nonsyn | aCT | aTC | 7405 | 2 | 0.000270088 | 25462-25464 | |
ORF3a | 24 | T24I | nonsyn | aCT | aTA | 7405 | 1 | 0.000135044 | 25462-25464 |
Details of the mutation T24I 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 |
ORF3a | 24 | T24I | aCt | aTt | 7402 | 7405 | All | 0.001416 |
ORF3a | 24 | T24I | aCT | aTC | 2 | 7405 | All | 0 |
ORF3a | 24 | T24I | aCT | aTA | 1 | 7405 | All | 0 |
ORF3a | 24 | T24I | aCt | aTt | 1744 | 1744 | AY.3 | 0.017347 |
ORF3a | 24 | T24I | aCt | aTt | 1655 | 1655 | AY.4 | 0.002576 |
ORF3a | 24 | T24I | aCt | aTt | 629 | 629 | B.1.1.7 | 0.000563 |
ORF3a | 24 | T24I | aCt | aTt | 559 | 559 | B.1.36.31 | 0.978984 |
ORF3a | 24 | T24I | aCt | aTt | 192 | 192 | AY.43 | 0.000851 |
ORF3a | 24 | T24I | aCt | aTt | 181 | 181 | B.1.617.2 | 0.000682 |
ORF3a | 24 | T24I | aCt | aTt | 172 | 172 | P.1 | 0.00271 |
ORF3a | 24 | T24I | aCt | aTt | 159 | 159 | B.1.351 | 0.004727 |
ORF3a | 24 | T24I | aCt | aTt | 150 | 150 | AY.44 | 0.000913 |
ORF3a | 24 | T24I | aCt | aTt | 139 | 139 | B.1 | 0.001273 |
ORF3a | 24 | T24I | aCt | aTt | 126 | 126 | AY.103 | 0.000782 |
ORF3a | 24 | T24I | aCt | aTt | 93 | 93 | B.1.2 | 0.000819 |
ORF3a | 24 | T24I | aCt | aTt | 92 | 92 | B.1.1 | 0.001669 |
ORF3a | 24 | T24I | aCt | aTt | 66 | 66 | AT.1 | 0.338462 |
ORF3a | 24 | T24I | aCt | aTt | 63 | 63 | B.1.351.2 | 0.019062 |
ORF3a | 24 | T24I | aCt | aTt | 59 | 59 | AY.25 | 0.000355 |
ORF3a | 24 | T24I | aCt | aTt | 59 | 59 | B.1.598 | 1 |
ORF3a | 24 | T24I | aCt | aTt | 52 | 52 | AY.27 | 0.003365 |
ORF3a | 24 | T24I | aCt | aTt | 52 | 52 | AY.47 | 0.001617 |
ORF3a | 24 | T24I | aCt | aTt | 51 | 51 | AY.26 | 0.001444 |
ORF3a | 24 | T24I | aCt | aTt | 50 | 50 | AY.23 | 0.003487 |
ORF3a | 24 | T24I | aCt | aTt | 50 | 50 | B.1.619 | 0.043554 |
ORF3a | 24 | T24I | aCt | aTt | 45 | 45 | B.1.177.86 | 0.008255 |
ORF3a | 24 | T24I | aCt | aTt | 44 | 44 | P.1.14 | 0.002103 |
ORF3a | 24 | T24I | aCt | aTt | 41 | 41 | B.1.221 | 0.002912 |
ORF3a | 24 | T24I | aCt | aTt | 38 | 38 | AY.33 | 0.002538 |
ORF3a | 24 | T24I | aCt | aTt | 30 | 31 | AY.39 | 0.000741 |
ORF3a | 24 | T24I | aCT | aTA | 1 | 31 | AY.39 | 0.000025 |
ORF3a | 24 | T24I | aCt | aTt | 29 | 29 | AY.102 | 0.000769 |
ORF3a | 24 | T24I | aCt | aTt | 28 | 28 | B.1.1.28 | 0.008715 |
ORF3a | 24 | T24I | aCt | aTt | 28 | 28 | B.1.177 | 0.000369 |
ORF3a | 24 | T24I | aCt | aTt | 28 | 28 | P.1.7 | 0.00894 |
ORF3a | 24 | T24I | aCt | aTt | 25 | 25 | AY.53 | 0.007188 |
ORF3a | 24 | T24I | aCt | aTt | 21 | 21 | AY.7 | 0.004116 |
ORF3a | 24 | T24I | aCt | aTt | 21 | 21 | AY.92 | 0.006033 |
ORF3a | 24 | T24I | aCt | aTt | 21 | 21 | B.1.240 | 0.004527 |
ORF3a | 24 | T24I | aCt | aTt | 20 | 20 | C.35 | 0.01548 |
ORF3a | 24 | T24I | aCt | aTt | 20 | 20 | C.37 | 0.002321 |
ORF3a | 24 | T24I | aCt | aTt | 19 | 19 | AY.20 | 0.000738 |
ORF3a | 24 | T24I | aCt | aTt | 17 | 17 | AY.120 | 0.000632 |
ORF3a | 24 | T24I | aCt | aTt | 16 | 16 | B.1.276 | 0.271186 |
ORF3a | 24 | T24I | aCt | aTt | 15 | 15 | B.1.429 | 0.000353 |
ORF3a | 24 | T24I | aCt | aTt | 14 | 14 | AY.100 | 0.000644 |
ORF3a | 24 | T24I | aCt | aTt | 14 | 14 | B.1.36 | 0.002043 |
ORF3a | 24 | T24I | aCt | aTt | 14 | 14 | B.1.525 | 0.001584 |
ORF3a | 24 | T24I | aCt | aTt | 13 | 13 | AY.46 | 0.001353 |
ORF3a | 24 | T24I | aCt | aTt | 13 | 13 | AY.5 | 0.000268 |
ORF3a | 24 | T24I | aCt | aTt | 13 | 13 | AY.98.1 | 0.00063 |
ORF3a | 24 | T24I | aCt | aTt | 12 | 12 | AY.99.2 | 0.001106 |
ORF3a | 24 | T24I | aCt | aTt | 11 | 11 | AY.4.2 | 0.000239 |
ORF3a | 24 | T24I | aCt | aTt | 11 | 11 | AY.42 | 0.000443 |
ORF3a | 24 | T24I | aCt | aTt | 11 | 11 | B.1.36.8 | 0.011 |
ORF3a | 24 | T24I | aCt | aTt | 10 | 10 | B.1.258 | 0.000665 |
ORF3a | 24 | T24I | aCt | aTt | 9 | 9 | AD.2 | 0.001971 |
ORF3a | 24 | T24I | aCt | aTt | 9 | 9 | AY.117 | 0.000761 |
ORF3a | 24 | T24I | aCt | aTt | 9 | 9 | AY.121 | 0.001218 |
ORF3a | 24 | T24I | aCt | aTt | 9 | 9 | AY.16 | 0.003417 |
ORF3a | 24 | T24I | aCt | aTt | 9 | 9 | AY.34 | 0.000873 |
ORF3a | 24 | T24I | aCt | aTt | 9 | 9 | B.1.160 | 0.000281 |
ORF3a | 24 | T24I | aCt | aTt | 8 | 8 | P.1.15 | 0.001859 |
ORF3a | 24 | T24I | aCt | aTt | 8 | 8 | P.7 | 0.034934 |
ORF3a | 24 | T24I | aCt | aTt | 7 | 7 | AY.45 | 0.000852 |
ORF3a | 24 | T24I | aCt | aTt | 7 | 7 | AY.75 | 0.000392 |
ORF3a | 24 | T24I | aCt | aTt | 7 | 7 | B.1.36.17 | 0.003458 |
ORF3a | 24 | T24I | aCt | aTt | 7 | 7 | P.2 | 0.001306 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | AY.113 | 0.000854 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | AY.29 | 0.000095 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | AY.39.1 | 0.000238 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | AY.46.6 | 0.000433 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | AY.6 | 0.000247 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | AY.72 | 0.008163 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | AY.9.2 | 0.00022 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | B.1.1.519 | 0.000238 |
ORF3a | 24 | T24I | aCt | aTt | 6 | 6 | B.1.466.2 | 0.002347 |
ORF3a | 24 | T24I | aCt | aTt | 5 | 5 | AY.119 | 0.000177 |
ORF3a | 24 | T24I | aCt | aTt | 5 | 5 | AY.61 | 0.000524 |
ORF3a | 24 | T24I | aCt | aTt | 5 | 5 | B.1.36.29 | 0.002587 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | AY.14 | 0.000352 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | AY.3.1 | 0.000341 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | AY.46.5 | 0.000794 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | B.1.1.10 | 0.004459 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | B.1.1.258 | 0.013029 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | B.1.1.370 | 0.050633 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | B.1.1.433 | 0.005698 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | B.1.596 | 0.000349 |
ORF3a | 24 | T24I | aCt | aTt | 4 | 4 | B.1.632 | 0.026846 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.101 | 0.001471 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.116 | 0.00086 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.13 | 0.000483 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.32 | 0.001597 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.34.1 | 0.00153 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.41 | 0.000882 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.48 | 0.001395 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.54 | 0.000286 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | AY.98 | 0.000237 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | B.1.1.317 | 0.001235 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | B.1.396 | 0.002117 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | B.1.526 | 0.000071 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | P.1.10 | 0.000808 |
ORF3a | 24 | T24I | aCt | aTt | 3 | 3 | Q.8 | 0.000495 |
ORF3a | 24 | T24I | aCT | aTC | 2 | 2 | 0.111111 | |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.111 | 0.000366 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.116.1 | 0.000623 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.4.2.1 | 0.000298 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.4.4 | 0.000818 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.5.3 | 0.000675 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.5.4 | 0.000553 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.55 | 0.001835 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.70 | 0.000417 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.84 | 0.000875 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | AY.9 | 0.000135 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B | 0.000256 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.1.170 | 0.002494 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.177.23 | 0.006472 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.177.33 | 0.003289 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.243 | 0.000139 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.422 | 0.001625 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.428 | 0.002041 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.438.1 | 0.000215 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.517.1 | 0.010526 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.595 | 0.000522 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.612 | 0.005305 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.617.1 | 0.000258 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.1.621 | 0.000177 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | B.40 | 0.000729 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | D.2 | 0.00015 |
ORF3a | 24 | T24I | aCt | aTt | 2 | 2 | P.1.12 | 0.000968 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | A.2 | 0.000662 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | A.5 | 0.001923 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AU.1 | 0.001266 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.108 | 0.001103 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.118 | 0.000063 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.120.1 | 0.000321 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.19 | 0.00114 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.24 | 0.000431 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.29.1 | 0.000221 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.35 | 0.000233 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.36 | 0.000148 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.37 | 0.000316 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.38 | 0.000499 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.4.5 | 0.000107 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.46.2 | 0.000635 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.46.4 | 0.000165 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.5.1 | 0.003759 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.51 | 0.000909 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.52 | 0.000814 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.59 | 0.00053 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.62 | 0.000436 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.74 | 0.000116 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.9.1 | 0.000084 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.93 | 0.000273 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.95 | 0.000761 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | AY.96 | 0.002075 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.1 | 0.000327 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.174 | 0.003378 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.207 | 0.001182 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.222 | 0.000204 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.231 | 0.003096 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.294 | 0.001266 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.37 | 0.000193 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.375 | 0.011905 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.398 | 0.003226 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.409 | 0.002833 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.51 | 0.001718 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.525 | 0.005464 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.1.528 | 0.004808 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.157 | 0.002985 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.177.18 | 0.00116 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.177.21 | 0.000076 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.177.32 | 0.00135 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.177.80 | 0.001912 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.206 | 0.000816 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.214.2 | 0.0006 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.234 | 0.000132 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.247 | 0.014925 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.258.3 | 0.001675 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.320 | 0.001245 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.323 | 0.020833 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.348 | 0.018182 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.349 | 0.000715 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.361 | 0.001289 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.367 | 0.000792 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.397 | 0.004854 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.409 | 0.000781 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.425 | 0.002994 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.427 | 0.00005 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.507 | 0.011236 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.517 | 0.000427 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.1.600 | 0.005848 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.6.6 | 0.000889 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.6.8 | 0.008264 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | B.61 | 0.005747 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | C.14 | 0.004329 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | C.8 | 0.004464 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | P.1.10.1 | 0.00813 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | P.1.16 | 0.000374 |
ORF3a | 24 | T24I | aCt | aTt | 1 | 1 | R.1 | 0.00009 |
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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