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 |
S | 386 | K386K | syn | aaA | aaG | 161 | 161 | 1 | 22718-22720 | |
S | 386 | K386del | del | AAA | --- | 77 | 77 | 1 | 22718-22720 | |
S | 386 | K386R | nonsyn | aAa | aGa | 11 | 11 | 1 | 22718-22720 | |
S | 386 | K386del1 | del | Aaa | -aa | 10 | 8 | 0.8 | 22718-22720 | |
S | 386 | K386del1 | del | AAa | -Ga | 10 | 1 | 0.1 | 22718-22720 | |
S | 386 | K386del1 | del | AAA | -NN | 10 | 1 | 0.1 | 22718-22720 | |
S | 386 | K386E | nonsyn | Aaa | Gaa | 8 | 8 | 1 | 22718-22720 | |
S | 386 | K386X | nonsyn | Aaa | Taa | 4 | 4 | 1 | 22718-22720 | |
S | 386 | K386L | nonsyn | AAa | TTa | 3 | 3 | 1 | 22718-22720 | |
S | 386 | K386del2 | del | aAA | a-- | 3 | 2 | 0.666667 | 22718-22720 | |
S | 386 | K386del2 | del | AAa | --a | 3 | 1 | 0.333333 | 22718-22720 | |
S | 386 | K386Y | nonsyn | AaA | TaC | 2 | 2 | 1 | 22718-22720 | |
S | 386 | K386I | nonsyn | aAa | aTa | 2 | 2 | 1 | 22718-22720 | |
S | 386 | K386Q | nonsyn | Aaa | Caa | 2 | 2 | 1 | 22718-22720 | |
S | 386 | K386N | nonsyn | aaA | aaC | 2 | 1 | 0.5 | 22718-22720 | |
S | 386 | K386T | nonsyn | aAa | aCa | 2 | 1 | 0.5 | 22718-22720 | |
S | 386 | K386T | nonsyn | aAA | aCG | 2 | 1 | 0.5 | 22718-22720 | |
S | 386 | K386N | nonsyn | aaA | aaT | 2 | 1 | 0.5 | 22718-22720 |
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 |
S | 386 | K386K | aaA | aaG | 161 | 161 | All | 0.000031 |
S | 386 | K386del | AAA | --- | 77 | 77 | All | 0.000015 |
S | 386 | K386K | aaA | aaG | 48 | 48 | B.1.1.33 | 0.020202 |
S | 386 | K386K | aaA | aaG | 34 | 34 | N.7 | 1 |
S | 386 | K386K | aaA | aaG | 19 | 19 | AY.4 | 0.00003 |
S | 386 | K386del | AAA | --- | 19 | 19 | B.1.1.7 | 0.000017 |
S | 386 | K386K | aaA | aaG | 12 | 12 | B.1.2 | 0.000106 |
S | 386 | K386R | aAa | aGa | 11 | 11 | All | 0.000002 |
S | 386 | K386del1 | Aaa | -aa | 8 | 10 | All | 0.000002 |
S | 386 | K386del1 | AAA | -NN | 1 | 10 | All | 0 |
S | 386 | K386del1 | AAa | -Ga | 1 | 10 | All | 0 |
S | 386 | K386K | aaA | aaG | 10 | 10 | B.1.1.7 | 0.000009 |
S | 386 | K386E | Aaa | Gaa | 8 | 8 | All | 0.000002 |
S | 386 | K386del | AAA | --- | 6 | 6 | AY.25 | 0.000036 |
S | 386 | K386del | AAA | --- | 5 | 5 | B.1 | 0.000046 |
S | 386 | K386del | AAA | --- | 5 | 5 | B.1.258 | 0.000333 |
S | 386 | K386X | Aaa | Taa | 4 | 4 | All | 0.000001 |
S | 386 | K386K | aaA | aaG | 4 | 4 | AY.25 | 0.000024 |
S | 386 | K386del | AAA | --- | 4 | 4 | AY.4 | 0.000006 |
S | 386 | K386del | AAA | --- | 4 | 4 | AY.43 | 0.000018 |
S | 386 | K386del1 | Aaa | -aa | 4 | 4 | B.1 | 0.000037 |
S | 386 | K386K | aaA | aaG | 4 | 4 | B.1.1.306 | 0.001754 |
S | 386 | K386L | AAa | TTa | 3 | 3 | All | 0.000001 |
S | 386 | K386del2 | aAA | a-- | 2 | 3 | All | 0 |
S | 386 | K386del2 | AAa | --a | 1 | 3 | All | 0 |
S | 386 | K386K | aaA | aaG | 3 | 3 | AY.43 | 0.000013 |
S | 386 | K386Y | AaA | TaC | 2 | 2 | 0.111111 | |
S | 386 | K386del | AAA | --- | 2 | 2 | 0.111111 | |
S | 386 | K386E | Aaa | Gaa | 2 | 2 | 0.111111 | |
S | 386 | K386I | aAa | aTa | 2 | 2 | All | 0 |
S | 386 | K386Y | AaA | TaC | 2 | 2 | All | 0 |
S | 386 | K386Q | Aaa | Caa | 2 | 2 | All | 0 |
S | 386 | K386T | aAA | aCG | 1 | 2 | All | 0 |
S | 386 | K386N | aaA | aaT | 1 | 2 | All | 0 |
S | 386 | K386N | aaA | aaC | 1 | 2 | All | 0 |
S | 386 | K386T | aAa | aCa | 1 | 2 | All | 0 |
S | 386 | K386K | aaA | aaG | 2 | 2 | AY.103 | 0.000012 |
S | 386 | K386K | aaA | aaG | 2 | 2 | AY.120 | 0.000074 |
S | 386 | K386del | AAA | --- | 2 | 2 | AY.4.5 | 0.000215 |
S | 386 | K386K | aaA | aaG | 2 | 2 | AY.46.3 | 0.001867 |
S | 386 | K386X | Aaa | Taa | 2 | 2 | B.1 | 0.000018 |
S | 386 | K386K | aaA | aaG | 2 | 2 | B.1.1 | 0.000036 |
S | 386 | K386K | aaA | aaG | 2 | 2 | B.1.1.63 | 0.000772 |
S | 386 | K386R | aAa | aGa | 2 | 2 | B.1.1.7 | 0.000002 |
S | 386 | K386del | AAA | --- | 2 | 2 | B.1.2 | 0.000018 |
S | 386 | K386del | AAA | --- | 2 | 2 | B.1.617.2 | 0.000008 |
S | 386 | K386del | AAA | --- | 2 | 2 | P.1.1 | 0.000635 |
S | 386 | K386L | AAa | TTa | 1 | 1 | A | 0.000387 |
S | 386 | K386T | aAa | aCa | 1 | 1 | A.2 | 0.000662 |
S | 386 | K386R | aAa | aGa | 1 | 1 | AE.3 | 0.032258 |
S | 386 | K386K | aaA | aaG | 1 | 1 | AY.107 | 0.000466 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.107 | 0.000466 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.109 | 0.00074 |
S | 386 | K386T | aAA | aCG | 1 | 1 | AY.110 | 0.000113 |
S | 386 | K386E | Aaa | Gaa | 1 | 1 | AY.117 | 0.000085 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.118 | 0.000063 |
S | 386 | K386del1 | Aaa | -aa | 1 | 1 | AY.120 | 0.000037 |
S | 386 | K386X | Aaa | Taa | 1 | 1 | AY.20 | 0.000039 |
S | 386 | K386K | aaA | aaG | 1 | 1 | AY.23 | 0.00007 |
S | 386 | K386Q | Aaa | Caa | 1 | 1 | AY.23 | 0.00007 |
S | 386 | K386N | aaA | aaT | 1 | 1 | AY.3 | 0.00001 |
S | 386 | K386K | aaA | aaG | 1 | 1 | AY.33 | 0.000067 |
S | 386 | K386K | aaA | aaG | 1 | 1 | AY.39 | 0.000025 |
S | 386 | K386E | Aaa | Gaa | 1 | 1 | AY.4 | 0.000002 |
S | 386 | K386del1 | Aaa | -aa | 1 | 1 | AY.43 | 0.000004 |
S | 386 | K386R | aAa | aGa | 1 | 1 | AY.43 | 0.000004 |
S | 386 | K386K | aaA | aaG | 1 | 1 | AY.54 | 0.000095 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.59 | 0.00053 |
S | 386 | K386R | aAa | aGa | 1 | 1 | AY.59 | 0.00053 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.67 | 0.000464 |
S | 386 | K386K | aaA | aaG | 1 | 1 | AY.69 | 0.000187 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.72 | 0.001361 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.9 | 0.000068 |
S | 386 | K386K | aaA | aaG | 1 | 1 | AY.9.2 | 0.000037 |
S | 386 | K386del | AAA | --- | 1 | 1 | AY.9.2 | 0.000037 |
S | 386 | K386K | aaA | aaG | 1 | 1 | B | 0.000128 |
S | 386 | K386E | Aaa | Gaa | 1 | 1 | B.1 | 0.000009 |
S | 386 | K386L | AAa | TTa | 1 | 1 | B.1 | 0.000009 |
S | 386 | K386L | AAa | TTa | 1 | 1 | B.1.1 | 0.000018 |
S | 386 | K386I | aAa | aTa | 1 | 1 | B.1.1 | 0.000018 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.1 | 0.000018 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.1.137 | 0.0125 |
S | 386 | K386del1 | AAa | -Ga | 1 | 1 | B.1.1.221 | 0.010101 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.1.315 | 0.008475 |
S | 386 | K386del2 | aAA | a-- | 1 | 1 | B.1.1.318 | 0.000302 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.1.519 | 0.00004 |
S | 386 | K386del2 | AAa | --a | 1 | 1 | B.1.1.7 | 0.000001 |
S | 386 | K386I | aAa | aTa | 1 | 1 | B.1.1.7 | 0.000001 |
S | 386 | K386E | Aaa | Gaa | 1 | 1 | B.1.1.7 | 0.000001 |
S | 386 | K386K | aaA | aaG | 1 | 1 | B.1.110.3 | 0.000718 |
S | 386 | K386K | aaA | aaG | 1 | 1 | B.1.160.24 | 0.004425 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.160.29 | 0.004219 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.177 | 0.000013 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.177.18 | 0.00116 |
S | 386 | K386R | aAa | aGa | 1 | 1 | B.1.2 | 0.000009 |
S | 386 | K386del1 | AAA | -NN | 1 | 1 | B.1.222 | 0.001692 |
S | 386 | K386K | aaA | aaG | 1 | 1 | B.1.234 | 0.000132 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.242 | 0.018868 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.351 | 0.00003 |
S | 386 | K386R | aAa | aGa | 1 | 1 | B.1.356 | 0.001727 |
S | 386 | K386R | aAa | aGa | 1 | 1 | B.1.36 | 0.000146 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.36.29 | 0.000517 |
S | 386 | K386R | aAa | aGa | 1 | 1 | B.1.369 | 0.000285 |
S | 386 | K386E | Aaa | Gaa | 1 | 1 | B.1.400 | 0.000429 |
S | 386 | K386Q | Aaa | Caa | 1 | 1 | B.1.413 | 0.004255 |
S | 386 | K386R | aAa | aGa | 1 | 1 | B.1.427 | 0.00005 |
S | 386 | K386X | Aaa | Taa | 1 | 1 | B.1.429 | 0.000024 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.446 | 0.02 |
S | 386 | K386K | aaA | aaG | 1 | 1 | B.1.509 | 0.000866 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.526 | 0.000024 |
S | 386 | K386del1 | Aaa | -aa | 1 | 1 | B.1.546 | 0.003704 |
S | 386 | K386K | aaA | aaG | 1 | 1 | B.1.561 | 0.000397 |
S | 386 | K386R | aAa | aGa | 1 | 1 | B.1.575 | 0.000303 |
S | 386 | K386del1 | Aaa | -aa | 1 | 1 | B.1.617.1 | 0.000129 |
S | 386 | K386K | aaA | aaG | 1 | 1 | B.1.617.2 | 0.000004 |
S | 386 | K386N | aaA | aaC | 1 | 1 | B.1.617.2 | 0.000004 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.620 | 0.000946 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.1.621 | 0.000089 |
S | 386 | K386E | Aaa | Gaa | 1 | 1 | B.1.627 | 0.00202 |
S | 386 | K386del2 | aAA | a-- | 1 | 1 | B.34 | 0.013699 |
S | 386 | K386del | AAA | --- | 1 | 1 | B.6 | 0.00091 |
S | 386 | K386K | aaA | aaG | 1 | 1 | C.32 | 0.023256 |
S | 386 | K386K | aaA | aaG | 1 | 1 | C.37 | 0.000116 |
S | 386 | K386K | aaA | aaG | 1 | 1 | P.1 | 0.000016 |
S | 386 | K386del | AAA | --- | 1 | 1 | Q.2 | 0.000613 |
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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