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/nsp16 | 1 | S1S | S6799S | syn | tcT | tcC | 17353 | 17333 | 0.998847 | 20659-20661 |
ORF1ab/nsp16 | 1 | S1S | S6799S | syn | tcT | tcA | 17353 | 14 | 0.000806777 | 20659-20661 |
ORF1ab/nsp16 | 1 | S1S | S6799S | syn | tcT | tcG | 17353 | 5 | 0.000288135 | 20659-20661 |
ORF1ab/nsp16 | 1 | S1S | S6799S | syn | TCt | AGt | 17353 | 1 | 0.0000576269 | 20659-20661 |
Details of the mutation S1S 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/nsp16 | 1 | S1S | tcT | tcC | 17333 | 17353 | All | 0.003315 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 14 | 17353 | All | 0.000003 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcG | 5 | 17353 | All | 0.000001 |
ORF1ab/nsp16 | 1 | S1S | TCt | AGt | 1 | 17353 | All | 0 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 6566 | 6566 | B.1.177.12 | 0.996056 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 4573 | 4573 | B.1.177 | 0.060215 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1738 | 1738 | B.1.177.44 | 0.90192 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1344 | 1344 | B.1.177.35 | 0.928818 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1074 | 1074 | B.1.177.42 | 0.960644 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 643 | 643 | B.1.177.43 | 0.949778 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 398 | 398 | B.1.177.41 | 0.995 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 203 | 203 | B.1 | 0.001859 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 191 | 191 | B.1.177.40 | 0.984536 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 95 | 95 | B.1.177.38 | 0.989583 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 62 | 62 | B.1.177.36 | 1 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 62 | 62 | B.1.177.39 | 0.953846 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 46 | 46 | B.1.160.30 | 0.136905 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 42 | 42 | B.1.221 | 0.002983 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 32 | 33 | B.1.160 | 0.000998 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 1 | 33 | B.1.160 | 0.000031 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 33 | 33 | B.1.177.37 | 0.891892 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 19 | 19 | B.1.36 | 0.002772 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 17 | 17 | B.1.1 | 0.000308 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 12 | 17 | B.1.258 | 0.000799 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 5 | 17 | B.1.258 | 0.000333 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 15 | 15 | B.1.177.31 | 0.172414 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 14 | 14 | AY.14 | 0.001232 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 7 | 11 | B.1.1.7 | 0.000006 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 2 | 11 | B.1.1.7 | 0.000002 |
ORF1ab/nsp16 | 1 | S1S | TCt | AGt | 1 | 11 | B.1.1.7 | 0.000001 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcG | 1 | 11 | B.1.1.7 | 0.000001 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 10 | 10 | B.1.177.6 | 0.009766 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 8 | 8 | AY.20 | 0.000311 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 7 | 8 | AY.4 | 0.000011 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 1 | 8 | AY.4 | 0.000002 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 8 | 8 | AY.88 | 0.007073 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 8 | 8 | B.1.429 | 0.000188 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 7 | 7 | B.1.1.39 | 0.003568 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 7 | 7 | B.1.177.9 | 0.009321 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 6 | 6 | B | 0.000767 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 6 | 6 | B.1.160.32 | 0.025751 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 5 | 5 | B.1.416.1 | 0.007812 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 4 | 4 | B.1.177.73 | 0.002265 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 2 | 3 | AY.43 | 0.000009 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 3 | AY.43 | 0.000004 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 3 | 3 | AY.44 | 0.000018 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 3 | 3 | B.1.1.70 | 0.001023 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 3 | 3 | B.1.177.45 | 0.001144 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 3 | 3 | B.1.177.86 | 0.00055 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 3 | 3 | B.1.260 | 0.010033 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 1 | 2 | AY.103 | 0.000006 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 2 | AY.103 | 0.000006 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | AY.84 | 0.000875 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.160.10 | 0.016129 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.177.52 | 0.003515 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.177.57 | 0.000562 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.2 | 0.000018 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.222 | 0.003384 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.240 | 0.000431 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.609 | 0.000959 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 2 | 2 | B.1.617.2 | 0.000008 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcG | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcG | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcA | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | AY.94 | 0.000443 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.141 | 0.002012 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.170 | 0.001247 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.189 | 0.001513 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.343 | 0.020833 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.37 | 0.000193 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.1.521 | 0.005348 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.104 | 0.00369 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.160.16 | 0.000929 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.160.26 | 0.002421 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcG | 1 | 1 | B.1.160.29 | 0.004219 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.17 | 0.000821 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.23 | 0.003236 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.50 | 0.004695 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.65 | 0.000665 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.77 | 0.000726 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.177.89 | 0.02439 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.214.3 | 0.007143 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.233 | 0.014085 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.237 | 0.004975 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.284 | 0.013158 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.36.9 | 0.003215 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.473 | 0.019231 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcG | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.533 | 0.009615 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | B.1.78 | 0.008547 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | K.1 | 0.02381 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | P.3 | 0.001595 |
ORF1ab/nsp16 | 1 | S1S | tcT | tcC | 1 | 1 | Z.1 | 0.00289 |
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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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