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 | 116 | A116S | A6914S | nonsyn | Gca | Tca | 5666 | 5659 | 0.998765 | 21004-21006 |
ORF1ab/nsp16 | 116 | A116S | A6914S | nonsyn | GcA | TcT | 5666 | 4 | 0.000705965 | 21004-21006 |
ORF1ab/nsp16 | 116 | A116S | A6914S | nonsyn | GcA | TcC | 5666 | 3 | 0.000529474 | 21004-21006 |
Details of the mutation A116S 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 | 116 | A116S | Gca | Tca | 5659 | 5666 | All | 0.001082 |
ORF1ab/nsp16 | 116 | A116S | GcA | TcT | 4 | 5666 | All | 0.000001 |
ORF1ab/nsp16 | 116 | A116S | GcA | TcC | 3 | 5666 | All | 0.000001 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1185 | 1185 | AZ.2 | 0.972906 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1150 | 1150 | AZ.1 | 0.997398 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 626 | 626 | AZ.3 | 0.951368 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 526 | 526 | B.1.1.7 | 0.000471 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 223 | 223 | AY.4 | 0.000347 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 182 | 182 | B.1.2 | 0.001603 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 176 | 176 | B.1.617.2 | 0.000663 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 148 | 148 | B.1.1.318 | 0.044659 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 123 | 123 | P.1.14 | 0.00588 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 122 | 122 | AZ.2.1 | 0.99187 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 111 | 111 | P.1.7 | 0.035441 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 99 | 99 | AY.43 | 0.000439 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 92 | 92 | AY.26 | 0.002605 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 91 | 91 | B.1.525 | 0.010298 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 82 | 82 | AY.44 | 0.000499 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 69 | 69 | AY.103 | 0.000428 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 47 | 47 | B.1.1 | 0.000853 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 40 | 40 | B.1 | 0.000366 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 36 | 36 | AY.118 | 0.002255 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 32 | 32 | AY.102 | 0.000848 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 25 | 25 | AY.25 | 0.00015 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 23 | 23 | B.1.160 | 0.000717 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 21 | 21 | AU.2 | 0.050847 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 18 | 18 | AY.20 | 0.0007 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 18 | 18 | AY.29 | 0.000284 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 15 | 15 | AY.75 | 0.00084 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 15 | 15 | B.1.1.519 | 0.000596 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 14 | 14 | B | 0.001789 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 13 | 13 | B.1.429 | 0.000306 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 12 | 12 | B.1.177 | 0.000158 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 11 | 11 | A.29 | 0.058511 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 11 | 11 | AY.39 | 0.000272 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 10 | 10 | AY.100 | 0.00046 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 9 | 0.222222 | |
ORF1ab/nsp16 | 116 | A116S | GcA | TcT | 3 | 9 | 0.166667 | |
ORF1ab/nsp16 | 116 | A116S | GcA | TcC | 2 | 9 | 0.111111 | |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 9 | 9 | AY.119 | 0.000318 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 9 | 9 | AY.33 | 0.000601 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 9 | 9 | B.1.160.26 | 0.021792 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 8 | 8 | B.1.311 | 0.002197 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 8 | 8 | B.1.427 | 0.000404 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 8 | 8 | B.1.630 | 0.041885 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 7 | 7 | AY.12 | 0.002212 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 7 | 7 | C.14 | 0.030303 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 7 | 7 | P.1 | 0.00011 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 6 | 6 | AY.3 | 0.00006 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 6 | 6 | AY.4.2 | 0.00013 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 6 | 6 | B.1.1.291 | 0.004454 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 6 | 6 | B.1.526 | 0.000141 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 6 | 6 | B.1.596 | 0.000523 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 6 | 6 | N.5 | 0.010601 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 5 | 5 | AY.120.1 | 0.001605 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 5 | 5 | AY.42 | 0.000201 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 5 | 5 | AY.47 | 0.000156 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 5 | 5 | AY.54 | 0.000477 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 5 | 5 | B.1.36 | 0.00073 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | AY.121 | 0.000541 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | AY.14 | 0.000352 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | AY.46.4 | 0.000658 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | AY.9.2 | 0.000147 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | AY.92 | 0.001149 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | B.1.1.284 | 0.00043 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 4 | B.1.221 | 0.000142 |
ORF1ab/nsp16 | 116 | A116S | GcA | TcT | 1 | 4 | B.1.221 | 0.000071 |
ORF1ab/nsp16 | 116 | A116S | GcA | TcC | 1 | 4 | B.1.221 | 0.000071 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | B.1.234 | 0.000528 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | B.1.258 | 0.000266 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 4 | 4 | B.1.621 | 0.000354 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | AY.108 | 0.003308 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | AY.117 | 0.000254 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | AY.120 | 0.000112 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | AY.37 | 0.000948 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | AY.4.5 | 0.000322 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | AY.72 | 0.004082 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | AY.9 | 0.000203 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | B.1.1.326 | 0.005282 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 3 | 3 | P.1.10 | 0.000808 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | A.30 | 0.285714 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | AY.46.6 | 0.000144 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | AY.55 | 0.001835 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | AY.75.1 | 0.000361 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | AY.9.1 | 0.000167 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | B.1.1.207 | 0.002364 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | B.1.1.317 | 0.000823 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | B.1.1.33 | 0.000842 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | B.1.1.337 | 0.007194 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | B.1.177.44 | 0.001038 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | C.16 | 0.002121 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | C.37 | 0.000232 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | C.38 | 0.016129 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 2 | 2 | D.2 | 0.00015 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | A.1 | 0.000282 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | A.28 | 0.002646 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AT.1 | 0.005128 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.105 | 0.000643 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.120.2.1 | 0.000498 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.16 | 0.00038 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.23.1 | 0.000417 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.35 | 0.000233 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.4.1 | 0.000737 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.41 | 0.000294 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.5.2 | 0.002463 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.5.4 | 0.000277 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.56 | 0.001605 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.1.129 | 0.009174 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.1.216 | 0.00089 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.1.28 | 0.000311 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.1.397 | 0.002252 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.147 | 0.000756 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.160.30 | 0.002976 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.160.33 | 0.004425 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.177.17 | 0.000821 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.177.53 | 0.002392 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.237 | 0.004975 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.251 | 0.021739 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.306 | 0.005714 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.36.29 | 0.000517 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.36.8 | 0.001 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.396 | 0.000706 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.530 | 0.007143 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.543 | 0.01 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.560 | 0.00463 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.565 | 0.00081 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.573 | 0.006098 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.576 | 0.000907 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.603 | 0.010638 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.618 | 0.004032 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | B.1.620 | 0.000946 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | P.1.16 | 0.000374 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | P.1.8 | 0.004785 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | Q.2 | 0.000613 |
ORF1ab/nsp16 | 116 | A116S | Gca | Tca | 1 | 1 | Q.8 | 0.000165 |
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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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