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 | 416 | S416L | nonsyn | tCa | tTa | 2543 | 2539 | 0.998427 | 29519-29521 | |
N | 416 | S416L | nonsyn | TCA | CTC | 2543 | 1 | 0.000393236 | 29519-29521 | |
N | 416 | S416L | nonsyn | tCA | tTG | 2543 | 1 | 0.000393236 | 29519-29521 | |
N | 416 | S416L | nonsyn | TCa | CTa | 2543 | 1 | 0.000393236 | 29519-29521 | |
N | 416 | S416L | nonsyn | TCA | CTT | 2543 | 1 | 0.000393236 | 29519-29521 |
Details of the mutation S416L 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 | 416 | S416L | tCa | tTa | 2539 | 2543 | All | 0.000486 |
N | 416 | S416L | TCA | CTC | 1 | 2543 | All | 0 |
N | 416 | S416L | TCa | CTa | 1 | 2543 | All | 0 |
N | 416 | S416L | TCA | CTT | 1 | 2543 | All | 0 |
N | 416 | S416L | tCA | tTG | 1 | 2543 | All | 0 |
N | 416 | S416L | tCa | tTa | 415 | 415 | AY.4 | 0.000646 |
N | 416 | S416L | tCa | tTa | 406 | 407 | B.1.1.7 | 0.000363 |
N | 416 | S416L | TCA | CTT | 1 | 407 | B.1.1.7 | 0.000001 |
N | 416 | S416L | tCa | tTa | 187 | 188 | B.1.617.2 | 0.000704 |
N | 416 | S416L | TCA | CTC | 1 | 188 | B.1.617.2 | 0.000004 |
N | 416 | S416L | tCa | tTa | 116 | 116 | B.1.2 | 0.001021 |
N | 416 | S416L | tCa | tTa | 115 | 115 | AY.103 | 0.000714 |
N | 416 | S416L | tCa | tTa | 84 | 84 | AY.44 | 0.000511 |
N | 416 | S416L | tCa | tTa | 80 | 80 | AY.43 | 0.000354 |
N | 416 | S416L | tCa | tTa | 77 | 77 | AY.25 | 0.000463 |
N | 416 | S416L | tCa | tTa | 74 | 74 | AY.3 | 0.000736 |
N | 416 | S416L | tCa | tTa | 49 | 49 | AY.119 | 0.00173 |
N | 416 | S416L | tCa | tTa | 49 | 49 | B.1.177.21 | 0.003747 |
N | 416 | S416L | tCa | tTa | 43 | 43 | B.1.526 | 0.001011 |
N | 416 | S416L | tCa | tTa | 40 | 40 | B.1.177 | 0.000527 |
N | 416 | S416L | tCa | tTa | 37 | 37 | B.1.429 | 0.000871 |
N | 416 | S416L | tCa | tTa | 31 | 31 | B.1 | 0.000284 |
N | 416 | S416L | tCa | tTa | 30 | 30 | AY.102 | 0.000795 |
N | 416 | S416L | tCa | tTa | 25 | 25 | AY.39 | 0.000618 |
N | 416 | S416L | tCa | tTa | 24 | 24 | B.1.351 | 0.000713 |
N | 416 | S416L | tCa | tTa | 24 | 24 | P.1 | 0.000378 |
N | 416 | S416L | tCa | tTa | 22 | 22 | R.1 | 0.00198 |
N | 416 | S416L | tCa | tTa | 20 | 20 | B.1.575 | 0.006068 |
N | 416 | S416L | tCa | tTa | 17 | 17 | AY.7 | 0.003332 |
N | 416 | S416L | tCa | tTa | 15 | 15 | B.1.1 | 0.000272 |
N | 416 | S416L | tCa | tTa | 15 | 15 | B.1.427 | 0.000757 |
N | 416 | S416L | tCa | tTa | 14 | 14 | AY.46.4 | 0.002303 |
N | 416 | S416L | tCa | tTa | 14 | 14 | AY.5 | 0.000289 |
N | 416 | S416L | tCa | tTa | 13 | 13 | B.1.324 | 0.020867 |
N | 416 | S416L | tCa | tTa | 12 | 12 | AY.26 | 0.00034 |
N | 416 | S416L | tCa | tTa | 12 | 12 | B.1.1.213 | 0.26087 |
N | 416 | S416L | tCa | tTa | 11 | 11 | AY.118 | 0.000689 |
N | 416 | S416L | tCa | tTa | 11 | 11 | AY.75 | 0.000616 |
N | 416 | S416L | tCa | tTa | 11 | 11 | B.1.36 | 0.001605 |
N | 416 | S416L | tCa | tTa | 11 | 11 | B.1.409 | 0.008594 |
N | 416 | S416L | tCa | tTa | 11 | 11 | B.1.525 | 0.001245 |
N | 416 | S416L | tCa | tTa | 10 | 10 | AY.29 | 0.000158 |
N | 416 | S416L | tCa | tTa | 10 | 10 | AY.4.2 | 0.000217 |
N | 416 | S416L | tCa | tTa | 10 | 10 | Q.1 | 0.001263 |
N | 416 | S416L | tCa | tTa | 9 | 9 | B.1.160 | 0.000281 |
N | 416 | S416L | tCa | tTa | 8 | 8 | A.23.1 | 0.005634 |
N | 416 | S416L | tCa | tTa | 8 | 8 | AY.114 | 0.001849 |
N | 416 | S416L | tCa | tTa | 8 | 8 | AY.20 | 0.000311 |
N | 416 | S416L | tCa | tTa | 8 | 8 | AY.98 | 0.000632 |
N | 416 | S416L | tCa | tTa | 8 | 8 | B.1.1.519 | 0.000318 |
N | 416 | S416L | tCa | tTa | 8 | 8 | P.1.6 | 0.015564 |
N | 416 | S416L | tCa | tTa | 7 | 7 | AY.42 | 0.000282 |
N | 416 | S416L | tCa | tTa | 7 | 7 | B.1.621 | 0.00062 |
N | 416 | S416L | tCa | tTa | 6 | 6 | AY.100 | 0.000276 |
N | 416 | S416L | tCa | tTa | 6 | 6 | AY.116.1 | 0.001869 |
N | 416 | S416L | tCa | tTa | 6 | 6 | B.1.596 | 0.000523 |
N | 416 | S416L | tCa | tTa | 6 | 6 | P.1.14 | 0.000287 |
N | 416 | S416L | tCa | tTa | 5 | 5 | AY.106 | 0.001674 |
N | 416 | S416L | tCa | tTa | 5 | 5 | AY.13 | 0.000805 |
N | 416 | S416L | tCa | tTa | 5 | 5 | AY.6 | 0.000206 |
N | 416 | S416L | tCa | tTa | 5 | 5 | AY.99.2 | 0.000461 |
N | 416 | S416L | tCa | tTa | 5 | 5 | B.1.637 | 0.000365 |
N | 416 | S416L | tCa | tTa | 5 | 5 | D.2 | 0.000375 |
N | 416 | S416L | tCa | tTa | 4 | 4 | AY.2 | 0.001425 |
N | 416 | S416L | tCa | tTa | 4 | 4 | AY.21 | 0.00759 |
N | 416 | S416L | tCa | tTa | 4 | 4 | AY.23 | 0.000279 |
N | 416 | S416L | tCa | tTa | 4 | 4 | AY.45 | 0.000487 |
N | 416 | S416L | tCa | tTa | 4 | 4 | AY.47 | 0.000124 |
N | 416 | S416L | tCa | tTa | 4 | 4 | AY.70 | 0.000834 |
N | 416 | S416L | tCa | tTa | 4 | 4 | AY.98.1 | 0.000194 |
N | 416 | S416L | tCa | tTa | 4 | 4 | B.1.1.1 | 0.001307 |
N | 416 | S416L | tCa | tTa | 4 | 4 | B.1.243 | 0.000278 |
N | 416 | S416L | tCa | tTa | 4 | 4 | B.1.258.17 | 0.000416 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.117 | 0.000254 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.14 | 0.000264 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.29.1 | 0.000662 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.33 | 0.0002 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.36 | 0.000445 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.46 | 0.000312 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.54 | 0.000286 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.59 | 0.001589 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.61 | 0.000314 |
N | 416 | S416L | tCa | tTa | 3 | 3 | AY.9.1 | 0.000251 |
N | 416 | S416L | tCa | tTa | 3 | 3 | B.1.1.318 | 0.000905 |
N | 416 | S416L | tCa | tTa | 3 | 3 | B.1.1.365 | 0.01676 |
N | 416 | S416L | tCa | tTa | 3 | 3 | B.1.127 | 0.006593 |
N | 416 | S416L | tCa | tTa | 3 | 3 | B.1.214.2 | 0.001799 |
N | 416 | S416L | tCa | tTa | 3 | 3 | B.1.221 | 0.000213 |
N | 416 | S416L | tCa | tTa | 3 | 3 | B.1.36.8 | 0.003 |
N | 416 | S416L | tCa | tTa | 3 | 3 | B.1.438.1 | 0.000322 |
N | 416 | S416L | tCa | tTa | 3 | 3 | C.37 | 0.000348 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.12 | 0.000632 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.27 | 0.000129 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.37 | 0.000632 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.4.1 | 0.001475 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.4.4 | 0.000818 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.4.5 | 0.000215 |
N | 416 | S416L | tCA | tTG | 1 | 2 | AY.40 | 0.000964 |
N | 416 | S416L | tCa | tTa | 1 | 2 | AY.40 | 0.000964 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.46.6 | 0.000144 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.5.3 | 0.000675 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.66 | 0.002139 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.7.1 | 0.000225 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.74 | 0.000231 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.75.1 | 0.000361 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.84 | 0.000875 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.88 | 0.001768 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.9.2 | 0.000073 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.94 | 0.000885 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.96 | 0.004149 |
N | 416 | S416L | tCa | tTa | 2 | 2 | AY.99.1 | 0.003106 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.1.214 | 0.000111 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.1.280 | 0.006173 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.1.284 | 0.000215 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.1.333 | 0.002153 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.1.416 | 0.00181 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.1.434 | 0.000697 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.1.70 | 0.000682 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.177.10 | 0.001756 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.177.54 | 0.001213 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.177.57 | 0.000562 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.177.86 | 0.000367 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.234 | 0.000264 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.258 | 0.000133 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.428 | 0.002041 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.469 | 0.00722 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.492 | 0.014085 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.509 | 0.001732 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.517 | 0.000854 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.617.1 | 0.000258 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.628 | 0.000705 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.630 | 0.010471 |
N | 416 | S416L | tCa | tTa | 2 | 2 | B.1.639 | 0.043478 |
N | 416 | S416L | tCa | tTa | 2 | 2 | P.1.10 | 0.000539 |
N | 416 | S416L | tCa | tTa | 2 | 2 | P.1.7 | 0.000639 |
N | 416 | S416L | tCa | tTa | 2 | 2 | P.3 | 0.00319 |
N | 416 | S416L | tCa | tTa | 2 | 2 | Q.4 | 0.00091 |
N | 416 | S416L | tCa | tTa | 2 | 2 | Q.8 | 0.00033 |
N | 416 | S416L | tCa | tTa | 1 | 1 | A.1 | 0.000282 |
N | 416 | S416L | tCa | tTa | 1 | 1 | A.2 | 0.000662 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AE.8 | 0.000489 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AH.2 | 0.012048 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.105 | 0.000643 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.108 | 0.001103 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.110 | 0.000113 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.113 | 0.000142 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.120 | 0.000037 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.16.1 | 0.00047 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.3.1 | 0.000085 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.34 | 0.000097 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.39.1 | 0.00004 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.46.1 | 0.001027 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.53 | 0.000288 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.55 | 0.000917 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.62 | 0.000436 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.63 | 0.000387 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.64 | 0.000595 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.65 | 0.000533 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.67 | 0.000464 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.68 | 0.000274 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.73 | 0.000665 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.91 | 0.00073 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.91.1 | 0.004065 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.95 | 0.000761 |
N | 416 | S416L | tCa | tTa | 1 | 1 | AY.97 | 0.001701 |
N | 416 | S416L | TCa | CTa | 1 | 1 | B | 0.000128 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.174 | 0.003378 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.222 | 0.000204 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.241 | 0.00207 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.243 | 0.004082 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.25 | 0.000569 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.277 | 0.000759 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.28 | 0.000311 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.291 | 0.000742 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.306 | 0.000438 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.317 | 0.000412 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.348 | 0.000796 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.369 | 0.000446 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.1.8 | 0.003584 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.160.10 | 0.008065 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.20 | 0.001517 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.43 | 0.001477 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.5 | 0.001242 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.58 | 0.001332 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.60 | 0.000218 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.75 | 0.001041 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.82 | 0.000477 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.177.9 | 0.001332 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.189 | 0.004292 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.221.1 | 0.002907 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.232 | 0.000537 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.258.11 | 0.000396 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.258.4 | 0.003448 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.265 | 0.001271 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.279 | 0.000514 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.298 | 0.002114 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.311 | 0.000275 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.320 | 0.001245 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.349 | 0.000715 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.36.17 | 0.000494 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.36.28 | 0.005747 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.36.29 | 0.000517 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.36.33 | 0.007576 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.361 | 0.001289 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.367 | 0.000792 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.396 | 0.000706 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.404 | 0.001302 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.441 | 0.009615 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.465 | 0.003802 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.497 | 0.000315 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.561 | 0.000397 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.595.4 | 0.007299 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.609 | 0.000479 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.610 | 0.003546 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.619.1 | 0.000641 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.620 | 0.000946 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.1.8 | 0.001972 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.3.1 | 0.001658 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.40 | 0.000364 |
N | 416 | S416L | tCa | tTa | 1 | 1 | B.55 | 0.00295 |
N | 416 | S416L | tCa | tTa | 1 | 1 | P.1.12 | 0.000484 |
N | 416 | S416L | tCa | tTa | 1 | 1 | P.2 | 0.000187 |
N | 416 | S416L | tCa | tTa | 1 | 1 | Q.3 | 0.000145 |
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
|