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/nsp6 | 261 | P261P | P3830P | syn | ccA | ccG | 372 | 228 | 0.612903 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261P | P3830P | syn | ccA | ccT | 372 | 135 | 0.362903 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261P | P3830P | syn | ccA | ccC | 372 | 9 | 0.0241935 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261S | P3830S | nonsyn | Cca | Tca | 78 | 78 | 1 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261del | P3830del | del | CCA | --- | 26 | 26 | 1 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261L | P3830L | nonsyn | cCa | cTa | 15 | 15 | 1 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261T | P3830T | nonsyn | Cca | Aca | 10 | 10 | 1 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261Q | P3830Q | nonsyn | cCa | cAa | 6 | 6 | 1 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261del2 | P3830del2 | del | cCA | c-- | 5 | 3 | 0.6 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261del2 | P3830del2 | del | CCa | --a | 5 | 2 | 0.4 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261A | P3830A | nonsyn | Cca | Gca | 4 | 4 | 1 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261del1 | P3830del1 | del | Cca | -ca | 2 | 1 | 0.5 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261del1 | P3830del1 | del | CCa | -Ta | 2 | 1 | 0.5 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261H | P3830H | nonsyn | cCA | cAC | 1 | 1 | 1 | 11753-11755 |
ORF1ab/nsp6 | 261 | P261V | P3830V | nonsyn | CCa | GTa | 1 | 1 | 1 | 11753-11755 |
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/nsp6 | 261 | P261P | ccA | ccG | 228 | 372 | All | 0.000044 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 135 | 372 | All | 0.000026 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 9 | 372 | All | 0.000002 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 78 | 78 | All | 0.000015 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 55 | 55 | B.1.1.347 | 1 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 38 | 48 | B.1.1.7 | 0.000034 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 9 | 48 | B.1.1.7 | 0.000008 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 1 | 48 | B.1.1.7 | 0.000001 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 35 | 40 | AY.4 | 0.000054 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 5 | 40 | AY.4 | 0.000008 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 31 | 31 | B.1.1.519 | 0.001231 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 28 | 28 | B.1.1.7 | 0.000025 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 26 | 26 | All | 0.000005 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 19 | 23 | B.1.1 | 0.000345 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 4 | 23 | B.1.1 | 0.000073 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 13 | 21 | B.1.617.2 | 0.000049 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 6 | 21 | B.1.617.2 | 0.000023 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 2 | 21 | B.1.617.2 | 0.000008 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 20 | 20 | AY.3 | 0.000199 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 10 | 19 | B.1 | 0.000092 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 7 | 19 | B.1 | 0.000064 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 2 | 19 | B.1 | 0.000018 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 18 | 18 | B.1.2 | 0.000158 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 9 | 16 | AY.103 | 0.000056 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 7 | 16 | AY.103 | 0.000043 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 15 | 15 | All | 0.000003 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 8 | 11 | AY.25 | 0.000048 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 3 | 11 | AY.25 | 0.000018 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 7 | 11 | B.1.177 | 0.000092 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 4 | 11 | B.1.177 | 0.000053 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 10 | 10 | All | 0.000002 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 10 | 10 | AY.3 | 0.000099 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 4 | 7 | AY.43 | 0.000018 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 3 | 7 | AY.43 | 0.000013 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 7 | 7 | B.1.177.60 | 0.001529 |
ORF1ab/nsp6 | 261 | P261Q | cCa | cAa | 6 | 6 | All | 0.000001 |
ORF1ab/nsp6 | 261 | P261del2 | cCA | c-- | 3 | 5 | All | 0.000001 |
ORF1ab/nsp6 | 261 | P261del2 | CCa | --a | 2 | 5 | All | 0 |
ORF1ab/nsp6 | 261 | P261A | Cca | Gca | 4 | 4 | All | 0.000001 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 4 | 4 | AY.25 | 0.000024 |
ORF1ab/nsp6 | 261 | P261Q | cCa | cAa | 4 | 4 | B.1 | 0.000037 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 4 | 4 | B.1 | 0.000037 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 4 | 4 | B.1 | 0.000037 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 4 | 4 | B.1.1 | 0.000073 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 4 | 4 | B.1.1.7 | 0.000004 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 3 | 3 | AY.117 | 0.000254 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 2 | 3 | AY.39 | 0.000049 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 1 | 3 | AY.39 | 0.000025 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 3 | 3 | B.1.1.7 | 0.000003 |
ORF1ab/nsp6 | 261 | P261del2 | cCA | c-- | 2 | 3 | B.1.1.7 | 0.000002 |
ORF1ab/nsp6 | 261 | P261del2 | CCa | --a | 1 | 3 | B.1.1.7 | 0.000001 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 3 | 3 | B.1.422 | 0.002437 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 3 | 3 | B.1.617.2 | 0.000011 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 2 | 2 | 0.111111 | |
ORF1ab/nsp6 | 261 | P261del1 | Cca | -ca | 1 | 2 | All | 0 |
ORF1ab/nsp6 | 261 | P261del1 | CCa | -Ta | 1 | 2 | All | 0 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 2 | 2 | AU.1 | 0.002532 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 2 | 2 | AY.42 | 0.00008 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 2 | AY.44 | 0.000006 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 2 | AY.44 | 0.000006 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 2 | 2 | AY.47 | 0.000062 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 2 | 2 | AY.93 | 0.000546 |
ORF1ab/nsp6 | 261 | P261A | Cca | Gca | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 2 | 2 | B.1.1.326 | 0.003521 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 2 | 2 | B.1.2 | 0.000018 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 2 | B.1.351 | 0.00003 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 2 | B.1.351 | 0.00003 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 2 | B.1.596 | 0.000087 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 2 | B.1.596 | 0.000087 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 2 | B.1.9 | 0.006173 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 1 | 2 | B.1.9 | 0.006173 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 2 | 2 | B.28 | 0.006557 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 1 | 1 | A | 0.000387 |
ORF1ab/nsp6 | 261 | P261V | CCa | GTa | 1 | 1 | All | 0 |
ORF1ab/nsp6 | 261 | P261H | cCA | cAC | 1 | 1 | All | 0 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | AY.28 | 0.00189 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | AY.7.1 | 0.000113 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | B | 0.000128 |
ORF1ab/nsp6 | 261 | P261V | CCa | GTa | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | B.1.1.153 | 0.001095 |
ORF1ab/nsp6 | 261 | P261del2 | CCa | --a | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | B.1.1.317 | 0.000412 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp6 | 261 | P261A | Cca | Gca | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp6 | 261 | P261del2 | cCA | c-- | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | B.1.177.9 | 0.001332 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp6 | 261 | P261del1 | CCa | -Ta | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp6 | 261 | P261Q | cCa | cAa | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | B.1.585 | 0.027778 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccT | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp6 | 261 | P261Q | cCa | cAa | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | B.1.606 | 0.006024 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp6 | 261 | P261A | Cca | Gca | 1 | 1 | B.1.612 | 0.002653 |
ORF1ab/nsp6 | 261 | P261H | cCA | cAC | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp6 | 261 | P261del1 | Cca | -ca | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | B.23 | 0.002924 |
ORF1ab/nsp6 | 261 | P261T | Cca | Aca | 1 | 1 | B.23 | 0.002924 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccC | 1 | 1 | B.35 | 0.007812 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | C.17 | 0.055556 |
ORF1ab/nsp6 | 261 | P261P | ccA | ccG | 1 | 1 | C.18 | 0.002591 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | C.36.3 | 0.000567 |
ORF1ab/nsp6 | 261 | P261L | cCa | cTa | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 1 | 1 | N.4 | 0.004255 |
ORF1ab/nsp6 | 261 | P261S | Cca | Tca | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp6 | 261 | P261del | CCA | --- | 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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