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 | 490 | F490S | nonsyn | tTt | tCt | 14547 | 14545 | 0.999862 | 23030-23032 | |
S | 490 | F490S | nonsyn | tTT | tCA | 14547 | 1 | 0.0000687427 | 23030-23032 | |
S | 490 | F490S | nonsyn | tTT | tCG | 14547 | 1 | 0.0000687427 | 23030-23032 |
Details of the mutation F490S 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 | 490 | F490S | tTt | tCt | 14545 | 14547 | All | 0.002782 |
S | 490 | F490S | tTT | tCG | 1 | 14547 | All | 0 |
S | 490 | F490S | tTT | tCA | 1 | 14547 | All | 0 |
S | 490 | F490S | tTt | tCt | 8414 | 8415 | C.37 | 0.976555 |
S | 490 | F490S | tTT | tCG | 1 | 8415 | C.37 | 0.000116 |
S | 490 | F490S | tTt | tCt | 4179 | 4180 | B.1.1.7 | 0.003741 |
S | 490 | F490S | tTT | tCA | 1 | 4180 | B.1.1.7 | 0.000001 |
S | 490 | F490S | tTt | tCt | 368 | 368 | C.37.1 | 0.963351 |
S | 490 | F490S | tTt | tCt | 172 | 172 | B.1.626 | 0.982857 |
S | 490 | F490S | tTt | tCt | 145 | 145 | AY.4 | 0.000226 |
S | 490 | F490S | tTt | tCt | 136 | 136 | Q.3 | 0.019724 |
S | 490 | F490S | tTt | tCt | 126 | 126 | B.1.617.2 | 0.000474 |
S | 490 | F490S | tTt | tCt | 78 | 78 | P.1.15 | 0.018123 |
S | 490 | F490S | tTt | tCt | 77 | 77 | B.1.1 | 0.001397 |
S | 490 | F490S | tTt | tCt | 72 | 72 | AY.103 | 0.000447 |
S | 490 | F490S | tTt | tCt | 70 | 70 | A.21 | 0.193906 |
S | 490 | F490S | tTt | tCt | 64 | 64 | B.1 | 0.000586 |
S | 490 | F490S | tTt | tCt | 52 | 52 | B.1.2 | 0.000458 |
S | 490 | F490S | tTt | tCt | 41 | 41 | Q.5 | 0.694915 |
S | 490 | F490S | tTt | tCt | 24 | 24 | AY.44 | 0.000146 |
S | 490 | F490S | tTt | tCt | 21 | 21 | AY.43 | 0.000093 |
S | 490 | F490S | tTt | tCt | 20 | 20 | AY.33 | 0.001336 |
S | 490 | F490S | tTt | tCt | 20 | 20 | B.1.177 | 0.000263 |
S | 490 | F490S | tTt | tCt | 15 | 15 | AY.102 | 0.000398 |
S | 490 | F490S | tTt | tCt | 15 | 15 | AY.26 | 0.000425 |
S | 490 | F490S | tTt | tCt | 15 | 15 | B.1.1.294 | 0.018987 |
S | 490 | F490S | tTt | tCt | 13 | 13 | B.1.1.528 | 0.0625 |
S | 490 | F490S | tTt | tCt | 12 | 12 | B.1.1.456 | 0.666667 |
S | 490 | F490S | tTt | tCt | 11 | 11 | AY.100 | 0.000506 |
S | 490 | F490S | tTt | tCt | 11 | 11 | B.1.160 | 0.000343 |
S | 490 | F490S | tTt | tCt | 11 | 11 | B.1.221 | 0.000781 |
S | 490 | F490S | tTt | tCt | 11 | 11 | P.1.1 | 0.003494 |
S | 490 | F490S | tTt | tCt | 10 | 10 | B.1.1.176 | 0.004394 |
S | 490 | F490S | tTt | tCt | 10 | 10 | B.1.1.519 | 0.000397 |
S | 490 | F490S | tTt | tCt | 10 | 10 | B.1.258 | 0.000665 |
S | 490 | F490S | tTt | tCt | 10 | 10 | B.1.564 | 0.004259 |
S | 490 | F490S | tTt | tCt | 10 | 10 | P.1.12 | 0.00484 |
S | 490 | F490S | tTt | tCt | 9 | 9 | AY.3 | 0.00009 |
S | 490 | F490S | tTt | tCt | 9 | 9 | AY.39 | 0.000222 |
S | 490 | F490S | tTt | tCt | 9 | 9 | AY.54 | 0.000858 |
S | 490 | F490S | tTt | tCt | 9 | 9 | B.1.1.28 | 0.002801 |
S | 490 | F490S | tTt | tCt | 8 | 8 | AY.20 | 0.000311 |
S | 490 | F490S | tTt | tCt | 8 | 8 | B.1.1.372 | 0.00551 |
S | 490 | F490S | tTt | tCt | 8 | 8 | P.1 | 0.000126 |
S | 490 | F490S | tTt | tCt | 7 | 7 | AY.25 | 0.000042 |
S | 490 | F490S | tTt | tCt | 7 | 7 | AY.45 | 0.000852 |
S | 490 | F490S | tTt | tCt | 7 | 7 | AY.56 | 0.011236 |
S | 490 | F490S | tTt | tCt | 7 | 7 | B.1.429 | 0.000165 |
S | 490 | F490S | tTt | tCt | 6 | 6 | B.1.1.348 | 0.004777 |
S | 490 | F490S | tTt | tCt | 6 | 6 | B.1.243 | 0.000418 |
S | 490 | F490S | tTt | tCt | 6 | 6 | Q.1 | 0.000758 |
S | 490 | F490S | tTt | tCt | 5 | 5 | B.1.1.33 | 0.002104 |
S | 490 | F490S | tTt | tCt | 5 | 5 | B.1.351 | 0.000149 |
S | 490 | F490S | tTt | tCt | 5 | 5 | B.1.427 | 0.000252 |
S | 490 | F490S | tTt | tCt | 5 | 5 | B.28 | 0.016393 |
S | 490 | F490S | tTt | tCt | 4 | 4 | AY.23 | 0.000279 |
S | 490 | F490S | tTt | tCt | 4 | 4 | AY.88 | 0.003537 |
S | 490 | F490S | tTt | tCt | 4 | 4 | B.1.1.161 | 0.014134 |
S | 490 | F490S | tTt | tCt | 4 | 4 | B.1.1.464 | 0.005891 |
S | 490 | F490S | tTt | tCt | 4 | 4 | B.1.214.2 | 0.002398 |
S | 490 | F490S | tTt | tCt | 4 | 4 | B.1.36 | 0.000584 |
S | 490 | F490S | tTt | tCt | 4 | 4 | B.1.36.29 | 0.002069 |
S | 490 | F490S | tTt | tCt | 4 | 4 | B.1.526 | 0.000094 |
S | 490 | F490S | tTt | tCt | 4 | 4 | C.39 | 0.075472 |
S | 490 | F490S | tTt | tCt | 3 | 3 | AY.120 | 0.000112 |
S | 490 | F490S | tTt | tCt | 3 | 3 | AY.3.1 | 0.000256 |
S | 490 | F490S | tTt | tCt | 3 | 3 | AY.4.2 | 0.000065 |
S | 490 | F490S | tTt | tCt | 3 | 3 | AY.48 | 0.001395 |
S | 490 | F490S | tTt | tCt | 3 | 3 | AY.98 | 0.000237 |
S | 490 | F490S | tTt | tCt | 3 | 3 | AY.98.1 | 0.000145 |
S | 490 | F490S | tTt | tCt | 3 | 3 | B.1.177.21 | 0.000229 |
S | 490 | F490S | tTt | tCt | 3 | 3 | R.1 | 0.00027 |
S | 490 | F490S | tTt | tCt | 2 | 2 | AY.110 | 0.000225 |
S | 490 | F490S | tTt | tCt | 2 | 2 | AY.116 | 0.000574 |
S | 490 | F490S | tTt | tCt | 2 | 2 | AY.117 | 0.000169 |
S | 490 | F490S | tTt | tCt | 2 | 2 | AY.16 | 0.000759 |
S | 490 | F490S | tTt | tCt | 2 | 2 | AY.75 | 0.000112 |
S | 490 | F490S | tTt | tCt | 2 | 2 | AY.75.1 | 0.000361 |
S | 490 | F490S | tTt | tCt | 2 | 2 | AY.90 | 0.001369 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.1.1 | 0.000653 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.1.232 | 0.00363 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.1.409 | 0.005666 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.104 | 0.00738 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.110.3 | 0.001437 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.239 | 0.002442 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.325 | 0.013793 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.521 | 0.00995 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.564.1 | 0.003155 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.596 | 0.000174 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.1.637 | 0.000146 |
S | 490 | F490S | tTt | tCt | 2 | 2 | B.6 | 0.00182 |
S | 490 | F490S | tTt | tCt | 2 | 2 | N.6 | 0.014184 |
S | 490 | F490S | tTt | tCt | 2 | 2 | P.1.10.1 | 0.01626 |
S | 490 | F490S | tTt | tCt | 2 | 2 | P.1.16 | 0.000748 |
S | 490 | F490S | tTt | tCt | 2 | 2 | Q.8 | 0.00033 |
S | 490 | F490S | tTt | tCt | 2 | 2 | W.4 | 0.002703 |
S | 490 | F490S | tTt | tCt | 1 | 1 | A | 0.000387 |
S | 490 | F490S | tTt | tCt | 1 | 1 | A.19 | 0.009434 |
S | 490 | F490S | tTt | tCt | 1 | 1 | A.23.1 | 0.000704 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AD.2 | 0.000219 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AE.8 | 0.000489 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.106 | 0.000335 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.121 | 0.000135 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.14 | 0.000088 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.24 | 0.000431 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.29 | 0.000016 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.32 | 0.000532 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.34 | 0.000097 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.35 | 0.000233 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.36 | 0.000148 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.42 | 0.00004 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.46.4 | 0.000165 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.52 | 0.000814 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.58 | 0.000907 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.6 | 0.000041 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.67 | 0.000464 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.68 | 0.000274 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.84 | 0.000437 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.85 | 0.000427 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.9.2 | 0.000037 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.93 | 0.000273 |
S | 490 | F490S | tTt | tCt | 1 | 1 | AY.99.2 | 0.000092 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B | 0.000128 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.121 | 0.002427 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.189 | 0.001513 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.214 | 0.000055 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.273 | 0.006757 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.284 | 0.000107 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.311 | 0.000358 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.354 | 0.004386 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.362 | 0.005618 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.37 | 0.000193 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.39 | 0.00051 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.412 | 0.007634 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.416 | 0.000905 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.433 | 0.001425 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.1.63 | 0.000386 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.134 | 0.005464 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.177.86 | 0.000183 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.210 | 0.002132 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.225 | 0.015385 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.236 | 0.002053 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.311 | 0.000275 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.324 | 0.001605 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.36.17 | 0.000494 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.396 | 0.000706 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.451 | 0.008197 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.470 | 0.001404 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.480 | 0.002488 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.517 | 0.000427 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.575 | 0.000303 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.577 | 0.000687 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.591 | 0.010638 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.1.628 | 0.000352 |
S | 490 | F490S | tTt | tCt | 1 | 1 | B.23 | 0.002924 |
S | 490 | F490S | tTt | tCt | 1 | 1 | C.14 | 0.004329 |
S | 490 | F490S | tTt | tCt | 1 | 1 | C.35 | 0.000774 |
S | 490 | F490S | tTt | tCt | 1 | 1 | C.36.3.1 | 0.002717 |
S | 490 | F490S | tTt | tCt | 1 | 1 | C.6 | 0.037037 |
S | 490 | F490S | tTt | tCt | 1 | 1 | D.3 | 0.005917 |
S | 490 | F490S | tTt | tCt | 1 | 1 | N.5 | 0.001767 |
S | 490 | F490S | tTt | tCt | 1 | 1 | P.1.10 | 0.000269 |
S | 490 | F490S | tTt | tCt | 1 | 1 | P.1.13 | 0.000898 |
S | 490 | F490S | tTt | tCt | 1 | 1 | Q.2 | 0.000613 |
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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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