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 |
ORF1ab/nsp3 | 1060 | K1060K | K1878K | syn | aaA | aaG | 342 | 342 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060R | K1878R | nonsyn | aAa | aGa | 126 | 126 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060E | K1878E | nonsyn | Aaa | Gaa | 27 | 27 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060del | K1878del | del | AAA | --- | 23 | 23 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060Q | K1878Q | nonsyn | Aaa | Caa | 13 | 13 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060N | K1878N | nonsyn | aaA | aaC | 10 | 5 | 0.5 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060N | K1878N | nonsyn | aaA | aaT | 10 | 5 | 0.5 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060I | K1878I | nonsyn | aAa | aTa | 8 | 7 | 0.875 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060I | K1878I | nonsyn | aAA | aTT | 8 | 1 | 0.125 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060T | K1878T | nonsyn | aAa | aCa | 7 | 7 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060X | K1878X | nonsyn | Aaa | Taa | 4 | 4 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060D | K1878D | nonsyn | AaA | GaT | 1 | 1 | 1 | 5897-5899 |
ORF1ab/nsp3 | 1060 | K1060Y | K1878Y | nonsyn | AaA | TaC | 1 | 1 | 1 | 5897-5899 |
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 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 342 | 342 | All | 0.000065 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 126 | 126 | All | 0.000024 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 103 | 103 | B.1.177.60 | 0.022499 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 46 | 46 | B.1.517 | 0.019641 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 45 | 45 | B.1.1.7 | 0.00004 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 39 | 39 | AY.20 | 0.001516 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 27 | 27 | All | 0.000005 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 26 | 26 | B.1.429 | 0.000612 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 23 | 23 | All | 0.000004 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 22 | 22 | AY.25 | 0.000132 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 19 | 19 | B.1.1.324 | 1 |
ORF1ab/nsp3 | 1060 | K1060Q | Aaa | Caa | 13 | 13 | All | 0.000002 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 13 | 13 | B.1.1.7 | 0.000012 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 13 | 13 | B.1.2 | 0.000114 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 12 | 12 | L.3 | 0.042553 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 11 | 11 | AY.44 | 0.000067 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaC | 5 | 10 | All | 0.000001 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaT | 5 | 10 | All | 0.000001 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 10 | 10 | AY.4 | 0.000016 |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 7 | 8 | All | 0.000001 |
ORF1ab/nsp3 | 1060 | K1060I | aAA | aTT | 1 | 8 | All | 0 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 7 | 7 | All | 0.000001 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 7 | 7 | B.1.1 | 0.000127 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 7 | 7 | P.1 | 0.00011 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 6 | 6 | AY.110 | 0.000676 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 6 | 6 | B.1.1.7 | 0.000005 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 5 | 5 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 1060 | K1060Q | Aaa | Caa | 5 | 5 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 5 | 5 | P.1 | 0.000079 |
ORF1ab/nsp3 | 1060 | K1060X | Aaa | Taa | 4 | 4 | All | 0.000001 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 4 | 4 | AY.6 | 0.000165 |
ORF1ab/nsp3 | 1060 | K1060Q | Aaa | Caa | 4 | 4 | AY.6 | 0.000165 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 4 | 4 | B.1.177 | 0.000053 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 4 | 4 | B.1.177 | 0.000053 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 4 | 4 | B.1.526 | 0.000094 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 4 | 4 | B.1.617.2 | 0.000015 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 3 | 3 | AY.103 | 0.000019 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 3 | 3 | AY.14 | 0.000264 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 3 | 3 | AY.3.1 | 0.000256 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 3 | 3 | B.1.621 | 0.000266 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaT | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaC | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1060 | K1060I | aAA | aTT | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 1 | 2 | 0.055556 | |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 2 | 2 | AY.102 | 0.000053 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 2 | 2 | AY.103 | 0.000012 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 2 | 2 | AY.44 | 0.000012 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 2 | 2 | AY.5 | 0.000041 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 2 | 2 | AY.99.2 | 0.000184 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaC | 1 | 2 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaT | 1 | 2 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1060 | K1060Q | Aaa | Caa | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 2 | 2 | B.1.164 | 0.029851 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaT | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 2 | 2 | B.1.369 | 0.00057 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 2 | 2 | P.1.15 | 0.000465 |
ORF1ab/nsp3 | 1060 | K1060X | Aaa | Taa | 1 | 1 | 0.055556 | |
ORF1ab/nsp3 | 1060 | K1060Y | AaA | TaC | 1 | 1 | 0.055556 | |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 1 | 1 | A.5 | 0.001923 |
ORF1ab/nsp3 | 1060 | K1060D | AaA | GaT | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1060 | K1060Y | AaA | TaC | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.115 | 0.005208 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp3 | 1060 | K1060X | Aaa | Taa | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp3 | 1060 | K1060Q | Aaa | Caa | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | AY.4.3 | 0.000842 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaC | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.57 | 0.000656 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.7.1 | 0.000113 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaC | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1060 | K1060X | Aaa | Taa | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.1.277 | 0.000759 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.1.348 | 0.000796 |
ORF1ab/nsp3 | 1060 | K1060Q | Aaa | Caa | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | B.1.1.63 | 0.000386 |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1060 | K1060T | aAa | aCa | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.177.23 | 0.003236 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.177.77 | 0.000726 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.409 | 0.000781 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.554 | 0.004405 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaT | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp3 | 1060 | K1060E | Aaa | Gaa | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | B.15 | 0.017544 |
ORF1ab/nsp3 | 1060 | K1060D | AaA | GaT | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp3 | 1060 | K1060R | aAa | aGa | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 1060 | K1060I | aAa | aTa | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 1060 | K1060X | Aaa | Taa | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 1060 | K1060N | aaA | aaC | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 1060 | K1060del | AAA | --- | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | R.1 | 0.00009 |
ORF1ab/nsp3 | 1060 | K1060K | aaA | aaG | 1 | 1 | U.2 | 0.008772 |
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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