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 |
N | 193 | S193T | nonsyn | aGt | aCt | 1560 | 1558 | 0.998718 | 28850-28852 | |
N | 193 | S193T | nonsyn | aGT | aCC | 1560 | 1 | 0.000641026 | 28850-28852 | |
N | 193 | S193T | nonsyn | aGT | aCA | 1560 | 1 | 0.000641026 | 28850-28852 |
Details of the mutation S193T 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 |
N | 193 | S193T | aGt | aCt | 1558 | 1560 | All | 0.000298 |
N | 193 | S193T | aGT | aCA | 1 | 1560 | All | 0 |
N | 193 | S193T | aGT | aCC | 1 | 1560 | All | 0 |
N | 193 | S193T | aGt | aCt | 401 | 402 | B.1.1.7 | 0.000359 |
N | 193 | S193T | aGT | aCC | 1 | 402 | B.1.1.7 | 0.000001 |
N | 193 | S193T | aGt | aCt | 131 | 131 | AY.43 | 0.00058 |
N | 193 | S193T | aGt | aCt | 129 | 129 | AY.4 | 0.000201 |
N | 193 | S193T | aGt | aCt | 99 | 99 | AY.44 | 0.000603 |
N | 193 | S193T | aGt | aCt | 86 | 86 | B.1.617.2 | 0.000324 |
N | 193 | S193T | aGt | aCt | 78 | 78 | B.1.9.5 | 0.443182 |
N | 193 | S193T | aGt | aCt | 66 | 66 | AY.14 | 0.005809 |
N | 193 | S193T | aGt | aCt | 63 | 63 | B.1.2 | 0.000555 |
N | 193 | S193T | aGt | aCt | 51 | 51 | AY.29 | 0.000804 |
N | 193 | S193T | aGt | aCt | 42 | 42 | AY.3 | 0.000418 |
N | 193 | S193T | aGt | aCt | 23 | 23 | AY.103 | 0.000143 |
N | 193 | S193T | aGt | aCt | 22 | 22 | B.1.1.50 | 0.014936 |
N | 193 | S193T | aGt | aCt | 19 | 19 | AY.100 | 0.000874 |
N | 193 | S193T | aGt | aCt | 19 | 19 | P.1 | 0.000299 |
N | 193 | S193T | aGt | aCt | 18 | 18 | B.40 | 0.006557 |
N | 193 | S193T | aGt | aCt | 17 | 17 | AY.62 | 0.007407 |
N | 193 | S193T | aGt | aCt | 16 | 16 | B.1.1.317 | 0.006587 |
N | 193 | S193T | aGt | aCt | 16 | 16 | B.1.429 | 0.000376 |
N | 193 | S193T | aGt | aCt | 14 | 14 | AY.102 | 0.000371 |
N | 193 | S193T | aGt | aCt | 13 | 13 | B.1 | 0.000119 |
N | 193 | S193T | aGt | aCt | 13 | 13 | B.1.1 | 0.000236 |
N | 193 | S193T | aGt | aCt | 10 | 10 | AY.20 | 0.000389 |
N | 193 | S193T | aGt | aCt | 9 | 9 | AY.39 | 0.000222 |
N | 193 | S193T | aGt | aCt | 9 | 9 | B.1.525 | 0.001018 |
N | 193 | S193T | aGt | aCt | 8 | 8 | AY.47 | 0.000249 |
N | 193 | S193T | aGt | aCt | 8 | 8 | B.1.621 | 0.000708 |
N | 193 | S193T | aGt | aCt | 7 | 7 | B.1.235 | 0.017632 |
N | 193 | S193T | aGt | aCt | 6 | 6 | A.2.5 | 0.002994 |
N | 193 | S193T | aGt | aCt | 6 | 6 | AY.120 | 0.000223 |
N | 193 | S193T | aGt | aCt | 6 | 6 | AY.5 | 0.000124 |
N | 193 | S193T | aGt | aCt | 6 | 6 | B.1.1.222 | 0.001224 |
N | 193 | S193T | aGt | aCt | 5 | 5 | B.1.1.28 | 0.001556 |
N | 193 | S193T | aGt | aCt | 5 | 5 | B.1.284 | 0.065789 |
N | 193 | S193T | aGt | aCt | 5 | 5 | B.1.305 | 0.010753 |
N | 193 | S193T | aGt | aCt | 5 | 5 | B.1.438.1 | 0.000536 |
N | 193 | S193T | aGt | aCt | 5 | 5 | P.1.14 | 0.000239 |
N | 193 | S193T | aGt | aCt | 4 | 4 | AY.25 | 0.000024 |
N | 193 | S193T | aGt | aCt | 4 | 4 | B.1.1.63 | 0.001543 |
N | 193 | S193T | aGt | aCt | 4 | 4 | B.1.351.3 | 0.003506 |
N | 193 | S193T | aGt | aCt | 4 | 4 | B.1.470 | 0.005618 |
N | 193 | S193T | aGt | aCt | 4 | 4 | B.1.526 | 0.000094 |
N | 193 | S193T | aGt | aCt | 4 | 4 | Q.8 | 0.00066 |
N | 193 | S193T | aGt | aCt | 3 | 3 | AY.119 | 0.000106 |
N | 193 | S193T | aGt | aCt | 3 | 3 | AY.34 | 0.000291 |
N | 193 | S193T | aGt | aCt | 3 | 3 | B.1.1.214 | 0.000166 |
N | 193 | S193T | aGt | aCt | 3 | 3 | B.1.1.519 | 0.000119 |
N | 193 | S193T | aGt | aCt | 3 | 3 | B.1.243 | 0.000209 |
N | 193 | S193T | aGt | aCt | 3 | 3 | B.1.596 | 0.000261 |
N | 193 | S193T | aGt | aCt | 3 | 3 | C.37 | 0.000348 |
N | 193 | S193T | aGT | aCA | 1 | 2 | 0.055556 | |
N | 193 | S193T | aGt | aCt | 1 | 2 | 0.055556 | |
N | 193 | S193T | aGt | aCt | 2 | 2 | AY.120.1 | 0.000642 |
N | 193 | S193T | aGt | aCt | 2 | 2 | AY.3.1 | 0.000171 |
N | 193 | S193T | aGt | aCt | 2 | 2 | AY.30 | 0.000791 |
N | 193 | S193T | aGt | aCt | 2 | 2 | AY.33 | 0.000134 |
N | 193 | S193T | aGt | aCt | 2 | 2 | AY.50 | 0.001599 |
N | 193 | S193T | aGt | aCt | 2 | 2 | AY.53 | 0.000575 |
N | 193 | S193T | aGt | aCt | 2 | 2 | AY.75 | 0.000112 |
N | 193 | S193T | aGt | aCt | 2 | 2 | B.1.1.33 | 0.000842 |
N | 193 | S193T | aGt | aCt | 2 | 2 | B.1.160 | 0.000062 |
N | 193 | S193T | aGt | aCt | 2 | 2 | B.1.177.17 | 0.001642 |
N | 193 | S193T | aGt | aCt | 2 | 2 | B.1.177.50 | 0.00939 |
N | 193 | S193T | aGt | aCt | 2 | 2 | B.1.221 | 0.000142 |
N | 193 | S193T | aGt | aCt | 2 | 2 | B.1.258 | 0.000133 |
N | 193 | S193T | aGt | aCt | 2 | 2 | D.2 | 0.00015 |
N | 193 | S193T | aGt | aCt | 2 | 2 | N.3 | 0.011628 |
N | 193 | S193T | aGt | aCt | 2 | 2 | Q.1 | 0.000253 |
N | 193 | S193T | aGt | aCt | 1 | 1 | A.23.1 | 0.000704 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.110 | 0.000113 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.111 | 0.000183 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.114 | 0.000231 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.116 | 0.000287 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.117 | 0.000085 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.13 | 0.000161 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.16.1 | 0.00047 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.19 | 0.00114 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.24 | 0.000431 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.26 | 0.000028 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.29.1 | 0.000221 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.39.1 | 0.00004 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.4.5 | 0.000107 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.41 | 0.000294 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.45 | 0.000122 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.5.1 | 0.003759 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.54 | 0.000095 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.59 | 0.00053 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.6 | 0.000041 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.65 | 0.000533 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.7.1 | 0.000113 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.74 | 0.000116 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.9 | 0.000068 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.9.1 | 0.000084 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.94 | 0.000443 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.98 | 0.000079 |
N | 193 | S193T | aGt | aCt | 1 | 1 | AY.99.2 | 0.000092 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B | 0.000128 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.1.161 | 0.003534 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.1.198 | 0.001468 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.1.216 | 0.00089 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.1.25 | 0.000569 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.1.275 | 0.011236 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.1.37 | 0.000193 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.1.46 | 0.004367 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.177.7 | 0.000165 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.177.73 | 0.000566 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.210 | 0.002132 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.240 | 0.000216 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.36 | 0.000146 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.545 | 0.014493 |
N | 193 | S193T | aGt | aCt | 1 | 1 | B.1.621.1 | 0.000506 |
N | 193 | S193T | aGt | aCt | 1 | 1 | P.1.7 | 0.000319 |
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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