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/nsp8 | 1 | A1A | A3943A | syn | gcT | gcC | 277 | 268 | 0.967509 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1A | A3943A | syn | gcT | gcG | 277 | 5 | 0.0180505 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1A | A3943A | syn | gcT | gcA | 277 | 4 | 0.0144404 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1S | A3943S | nonsyn | Gct | Tct | 140 | 140 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1V | A3943V | nonsyn | gCt | gTt | 14 | 14 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1D | A3943D | nonsyn | gCt | gAt | 11 | 11 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1del2 | A3943del2 | del | gCT | g-- | 11 | 9 | 0.818182 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1del2 | A3943del2 | del | GCt | --t | 11 | 2 | 0.181818 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1del | A3943del | del | GCT | --- | 7 | 7 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1del1 | A3943del1 | del | gcT | gc- | 6 | 6 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1T | A3943T | nonsyn | Gct | Act | 6 | 6 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1G | A3943G | nonsyn | gCt | gGt | 6 | 5 | 0.833333 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1G | A3943G | nonsyn | gCT | gGG | 6 | 1 | 0.166667 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1H | A3943H | nonsyn | GCt | CAt | 3 | 3 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1P | A3943P | nonsyn | Gct | Cct | 3 | 3 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1R | A3943R | nonsyn | GCT | AGA | 2 | 2 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1Q | A3943Q | nonsyn | GCT | CAG | 2 | 2 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1N | A3943N | nonsyn | GCt | AAt | 1 | 1 | 1 | 12092-12094 |
ORF1ab/nsp8 | 1 | A1C | A3943C | nonsyn | GCT | TGC | 1 | 1 | 1 | 12092-12094 |
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/nsp8 | 1 | A1A | gcT | gcC | 268 | 277 | All | 0.000051 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcG | 5 | 277 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcA | 4 | 277 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 140 | 140 | All | 0.000027 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 91 | 91 | B.1.1.437 | 0.947917 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 52 | 52 | B.1.1.7 | 0.000047 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 23 | 23 | AY.25 | 0.000138 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 22 | 22 | Q.1 | 0.002779 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 21 | 21 | B.1.1.7 | 0.000019 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 19 | 19 | AY.29 | 0.0003 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 16 | 16 | AY.5 | 0.00033 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 14 | 14 | All | 0.000003 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 12 | 13 | AY.4 | 0.000019 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcA | 1 | 13 | AY.4 | 0.000002 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 11 | 12 | AY.43 | 0.000049 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcA | 1 | 12 | AY.43 | 0.000004 |
ORF1ab/nsp8 | 1 | A1D | gCt | gAt | 11 | 11 | All | 0.000002 |
ORF1ab/nsp8 | 1 | A1del2 | gCT | g-- | 9 | 11 | All | 0.000002 |
ORF1ab/nsp8 | 1 | A1del2 | GCt | --t | 2 | 11 | All | 0 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 10 | 10 | B.1.2 | 0.000088 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 9 | 9 | AY.44 | 0.000055 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 9 | 9 | B.1.429 | 0.000212 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 8 | 8 | AY.4.2 | 0.000174 |
ORF1ab/nsp8 | 1 | A1del | GCT | --- | 7 | 7 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 7 | 7 | AY.46.5 | 0.001389 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 7 | 7 | B.1 | 0.000064 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 7 | 7 | B.1 | 0.000064 |
ORF1ab/nsp8 | 1 | A1T | Gct | Act | 6 | 6 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1del1 | gcT | gc- | 6 | 6 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1G | gCt | gGt | 5 | 6 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1G | gCT | gGG | 1 | 6 | All | 0 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 5 | 5 | AY.102 | 0.000133 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 5 | 5 | AY.23 | 0.000349 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 5 | 5 | B.1.617.2 | 0.000019 |
ORF1ab/nsp8 | 1 | A1D | gCt | gAt | 5 | 5 | P.1 | 0.000079 |
ORF1ab/nsp8 | 1 | A1H | GCt | CAt | 3 | 3 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1P | Gct | Cct | 3 | 3 | All | 0.000001 |
ORF1ab/nsp8 | 1 | A1del2 | gCT | g-- | 3 | 3 | AY.39.1 | 0.000119 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 3 | 3 | AY.43 | 0.000013 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 3 | 3 | B.1.177 | 0.00004 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 3 | 3 | B.1.2 | 0.000026 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcG | 2 | 3 | B.1.429 | 0.000047 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 3 | B.1.429 | 0.000024 |
ORF1ab/nsp8 | 1 | A1del | GCT | --- | 2 | 2 | 0.111111 | |
ORF1ab/nsp8 | 1 | A1del2 | GCt | --t | 2 | 2 | 0.111111 | |
ORF1ab/nsp8 | 1 | A1H | GCt | CAt | 2 | 2 | 0.111111 | |
ORF1ab/nsp8 | 1 | A1Q | GCT | CAG | 2 | 2 | 0.111111 | |
ORF1ab/nsp8 | 1 | A1G | gCt | gGt | 1 | 2 | 0.055556 | |
ORF1ab/nsp8 | 1 | A1G | gCT | gGG | 1 | 2 | 0.055556 | |
ORF1ab/nsp8 | 1 | A1R | GCT | AGA | 2 | 2 | All | 0 |
ORF1ab/nsp8 | 1 | A1Q | GCT | CAG | 2 | 2 | All | 0 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 2 | 2 | AY.102 | 0.000053 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcG | 2 | 2 | AY.20 | 0.000078 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp8 | 1 | A1del2 | gCT | g-- | 2 | 2 | AY.30 | 0.000791 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp8 | 1 | A1D | gCt | gAt | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp8 | 1 | A1del2 | gCT | g-- | 2 | 2 | AY.85 | 0.000854 |
ORF1ab/nsp8 | 1 | A1T | Gct | Act | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 2 | 2 | B.1.1.269 | 0.002706 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp8 | 1 | A1del | GCT | --- | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp8 | 1 | A1G | gCt | gGt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp8 | 1 | A1T | Gct | Act | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 2 | 2 | D.2 | 0.00015 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 2 | 2 | Q.8 | 0.00033 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 2 | 2 | V.2 | 0.064516 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcG | 1 | 1 | 0.055556 | |
ORF1ab/nsp8 | 1 | A1T | Gct | Act | 1 | 1 | 0.055556 | |
ORF1ab/nsp8 | 1 | A1N | GCt | AAt | 1 | 1 | All | 0 |
ORF1ab/nsp8 | 1 | A1C | GCT | TGC | 1 | 1 | All | 0 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp8 | 1 | A1del2 | gCT | g-- | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcA | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp8 | 1 | A1del1 | gcT | gc- | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp8 | 1 | A1del | GCT | --- | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp8 | 1 | A1del1 | gcT | gc- | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | AY.4.4 | 0.000409 |
ORF1ab/nsp8 | 1 | A1D | gCt | gAt | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp8 | 1 | A1H | GCt | CAt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.73 | 0.000665 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp8 | 1 | A1del2 | gCT | g-- | 1 | 1 | AY.79 | 0.001211 |
ORF1ab/nsp8 | 1 | A1G | gCt | gGt | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcA | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B | 0.000128 |
ORF1ab/nsp8 | 1 | A1P | Gct | Cct | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp8 | 1 | A1del1 | gcT | gc- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp8 | 1 | A1del | GCT | --- | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp8 | 1 | A1C | GCT | TGC | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp8 | 1 | A1P | Gct | Cct | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp8 | 1 | A1del1 | gcT | gc- | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.1.8 | 0.003584 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp8 | 1 | A1P | Gct | Cct | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | B.1.206 | 0.000816 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | B.1.260 | 0.003344 |
ORF1ab/nsp8 | 1 | A1D | gCt | gAt | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.36.7 | 0.004 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.371 | 0.001122 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.453 | 0.003236 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 1 | 1 | B.1.580 | 0.004065 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp8 | 1 | A1G | gCt | gGt | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp8 | 1 | A1R | GCT | AGA | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp8 | 1 | A1del1 | gcT | gc- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp8 | 1 | A1T | Gct | Act | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | B.6.6 | 0.000889 |
ORF1ab/nsp8 | 1 | A1R | GCT | AGA | 1 | 1 | C.17 | 0.055556 |
ORF1ab/nsp8 | 1 | A1del1 | gcT | gc- | 1 | 1 | C.36.3 | 0.000567 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp8 | 1 | A1del | GCT | --- | 1 | 1 | N.4 | 0.004255 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | N.5 | 0.001767 |
ORF1ab/nsp8 | 1 | A1N | GCt | AAt | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp8 | 1 | A1V | gCt | gTt | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp8 | 1 | A1S | Gct | Tct | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp8 | 1 | A1D | gCt | gAt | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp8 | 1 | A1A | gcT | gcC | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp8 | 1 | A1D | gCt | gAt | 1 | 1 | P.2 | 0.000187 |
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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