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 | 235 | K235R | K1053R | nonsyn | aAa | aGa | 219 | 218 | 0.995434 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235R | K1053R | nonsyn | aAA | aGG | 219 | 1 | 0.00456621 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235T | K1053T | nonsyn | aAa | aCa | 130 | 129 | 0.992308 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235T | K1053T | nonsyn | aAA | aCC | 130 | 1 | 0.00769231 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235E | K1053E | nonsyn | Aaa | Gaa | 103 | 103 | 1 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235K | K1053K | syn | aaA | aaG | 89 | 89 | 1 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235N | K1053N | nonsyn | aaA | aaC | 60 | 55 | 0.916667 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235N | K1053N | nonsyn | aaA | aaT | 60 | 5 | 0.0833333 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235Q | K1053Q | nonsyn | Aaa | Caa | 45 | 45 | 1 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235del | K1053del | del | AAA | --- | 21 | 21 | 1 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235I | K1053I | nonsyn | aAa | aTa | 2 | 2 | 1 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235del1 | K1053del1 | del | Aaa | -aa | 2 | 2 | 1 | 3422-3424 |
ORF1ab/nsp3 | 235 | K235del2 | K1053del2 | del | AAa | --a | 1 | 1 | 1 | 3422-3424 |
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 | 235 | K235R | aAa | aGa | 218 | 219 | All | 0.000042 |
ORF1ab/nsp3 | 235 | K235R | aAA | aGG | 1 | 219 | All | 0 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 136 | 136 | B.1.466.1 | 0.978417 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 129 | 130 | All | 0.000025 |
ORF1ab/nsp3 | 235 | K235T | aAA | aCC | 1 | 130 | All | 0 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 103 | 103 | All | 0.00002 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 100 | 100 | B.1.1.7 | 0.00009 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 89 | 89 | All | 0.000017 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 55 | 60 | All | 0.000011 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaT | 5 | 60 | All | 0.000001 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 53 | 53 | B.1.438.1 | 0.005685 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 45 | 45 | All | 0.000009 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 38 | 38 | B.1.1.7 | 0.000034 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 32 | 32 | AY.29.1 | 0.007056 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 21 | 21 | All | 0.000004 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 20 | 20 | AY.6 | 0.000823 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 16 | 16 | B.1.617.2 | 0.00006 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 14 | 14 | B.1.1.7 | 0.000013 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 14 | 14 | B.1.493 | 0.358974 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 10 | 10 | AY.29 | 0.000158 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 10 | 10 | AY.44 | 0.000061 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 10 | 10 | AY.46.5 | 0.001984 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 10 | 10 | B.1 | 0.000092 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 8 | 8 | AY.6 | 0.000329 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 7 | 7 | AY.4 | 0.000011 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 7 | 7 | B.1.617.2 | 0.000026 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 6 | 6 | AY.4 | 0.000009 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 6 | 6 | AY.4 | 0.000009 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 6 | 6 | AY.4 | 0.000009 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 6 | 6 | B.1 | 0.000055 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 5 | 6 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaT | 1 | 6 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 5 | 5 | AY.103 | 0.000031 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 5 | 5 | AY.103 | 0.000031 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 4 | 5 | B.1 | 0.000037 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaT | 1 | 5 | B.1 | 0.000009 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 5 | 5 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 5 | 5 | N.5 | 0.008834 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 4 | 4 | AY.39 | 0.000099 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 4 | 4 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 4 | 4 | B.1.617.2 | 0.000015 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 3 | 3 | AY.32 | 0.001597 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 3 | 3 | B.1.1.33 | 0.001263 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 3 | 3 | B.1.177 | 0.00004 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 3 | 3 | C.37 | 0.000348 |
ORF1ab/nsp3 | 235 | K235del1 | Aaa | -aa | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 235 | K235I | aAa | aTa | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 2 | 2 | AY.102 | 0.000053 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 2 | 2 | AY.103 | 0.000012 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 2 | 2 | AY.111 | 0.000366 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 2 | 2 | AY.113 | 0.000285 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 2 | 2 | AY.12 | 0.000632 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 2 | 2 | AY.3 | 0.00002 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 2 | 2 | AY.3.1 | 0.000171 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 2 | 2 | AY.44 | 0.000012 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 2 | 2 | AY.5 | 0.000041 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 2 | AY.85 | 0.000427 |
ORF1ab/nsp3 | 235 | K235T | aAA | aCC | 1 | 2 | AY.85 | 0.000427 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 2 | 2 | B.1.1.34 | 0.026316 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 2 | 2 | B.1.1.348 | 0.001592 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 2 | 2 | B.1.460 | 0.035714 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 2 | 2 | C.9 | 0.060606 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 2 | 2 | N.6 | 0.014184 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 2 | 2 | P.1.12 | 0.000968 |
ORF1ab/nsp3 | 235 | K235del2 | AAa | --a | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | AY.11 | 0.001339 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 1 | 1 | AY.29.1 | 0.000221 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaT | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | AY.35 | 0.000233 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | AY.51 | 0.000909 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 1 | 1 | AY.55 | 0.000917 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | AY.57 | 0.000656 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp3 | 235 | K235del2 | AAa | --a | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 235 | K235I | aAa | aTa | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 235 | K235R | aAA | aGG | 1 | 1 | B.1.1.139 | 0.022727 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | B.1.1.326 | 0.001761 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | B.1.1.464 | 0.001473 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 1 | 1 | B.1.1.526 | 0.003546 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 235 | K235del1 | Aaa | -aa | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | B.1.177.45 | 0.000381 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 1 | 1 | B.1.177.76 | 0.002494 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | B.1.221.4 | 0.004167 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | B.1.241 | 0.000812 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp3 | 235 | K235T | aAa | aCa | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 1 | 1 | B.1.389 | 0.001002 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaT | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaT | 1 | 1 | B.1.479 | 0.038462 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | B.1.560 | 0.00463 |
ORF1ab/nsp3 | 235 | K235del1 | Aaa | -aa | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp3 | 235 | K235N | aaA | aaC | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | B.1.630 | 0.005236 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | C.17 | 0.055556 |
ORF1ab/nsp3 | 235 | K235R | aAa | aGa | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp3 | 235 | K235E | Aaa | Gaa | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp3 | 235 | K235Q | Aaa | Caa | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp3 | 235 | K235I | aAa | aTa | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp3 | 235 | K235K | aaA | aaG | 1 | 1 | Q.4 | 0.000455 |
ORF1ab/nsp3 | 235 | K235del | AAA | --- | 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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