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 | F490L | nonsyn | Ttt | Ctt | 1540 | 1322 | 0.858442 | 23030-23032 |
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 |
S | 490 | F490L | Ttt | Ctt | 1322 | 1540 | All | 0.000253 |
S | 490 | F490L | Ttt | Ctt | 499 | 610 | B.1.1.7 | 0.000447 |
S | 490 | F490L | Ttt | Ctt | 185 | 196 | AY.4 | 0.000288 |
S | 490 | F490L | Ttt | Ctt | 60 | 70 | B.1.617.2 | 0.000226 |
S | 490 | F490L | Ttt | Ctt | 69 | 69 | AY.47 | 0.002146 |
S | 490 | F490L | Ttt | Ctt | 43 | 43 | AY.36 | 0.006373 |
S | 490 | F490L | Ttt | Ctt | 33 | 33 | AY.65 | 0.017591 |
S | 490 | F490L | Ttt | Ctt | 27 | 29 | AY.61 | 0.002829 |
S | 490 | F490L | Ttt | Ctt | 28 | 28 | AY.116.1 | 0.00872 |
S | 490 | F490L | Ttt | Ctt | 24 | 24 | AY.44 | 0.000146 |
S | 490 | F490L | Ttt | Ctt | 14 | 22 | AY.25 | 0.000084 |
S | 490 | F490L | Ttt | Ctt | 21 | 21 | B.1.177.86 | 0.003853 |
S | 490 | F490L | Ttt | Ctt | 7 | 17 | B.1 | 0.000064 |
S | 490 | F490L | Ttt | Ctt | 14 | 16 | AY.43 | 0.000062 |
S | 490 | F490L | Ttt | Ctt | 14 | 16 | B.1.1 | 0.000254 |
S | 490 | F490L | Ttt | Ctt | 13 | 16 | B.1.2 | 0.000114 |
S | 490 | F490L | Ttt | Ctt | 12 | 15 | AY.120 | 0.000446 |
S | 490 | F490L | Ttt | Ctt | 6 | 14 | AY.3 | 0.00006 |
S | 490 | F490L | Ttt | Ctt | 12 | 13 | AY.102 | 0.000318 |
S | 490 | F490L | Ttt | Ctt | 9 | 13 | AY.103 | 0.000056 |
S | 490 | F490L | Ttt | Ctt | 12 | 12 | B.1.177.60 | 0.002621 |
S | 490 | F490L | Ttt | Ctt | 6 | 10 | AY.5 | 0.000124 |
S | 490 | F490L | Ttt | Ctt | 10 | 10 | B.1.177 | 0.000132 |
S | 490 | F490L | Ttt | Ctt | 9 | 9 | AY.39.1 | 0.000357 |
S | 490 | F490L | Ttt | Ctt | 9 | 9 | AY.4.2 | 0.000195 |
S | 490 | F490L | Ttt | Ctt | 8 | 8 | A | 0.003096 |
S | 490 | F490L | Ttt | Ctt | 8 | 8 | AY.60 | 0.007505 |
S | 490 | F490L | Ttt | Ctt | 8 | 8 | AY.98.1 | 0.000387 |
S | 490 | F490L | Ttt | Ctt | 3 | 7 | 0.166667 | |
S | 490 | F490L | Ttt | Ctt | 7 | 7 | B.1.1.141 | 0.014085 |
S | 490 | F490L | Ttt | Ctt | 5 | 7 | B.1.160 | 0.000156 |
S | 490 | F490L | Ttt | Ctt | 7 | 7 | B.1.627 | 0.014141 |
S | 490 | F490L | Ttt | Ctt | 5 | 6 | AY.119 | 0.000177 |
S | 490 | F490L | Ttt | Ctt | 6 | 6 | AY.26 | 0.00017 |
S | 490 | F490L | Ttt | Ctt | 6 | 6 | B.6.6 | 0.005333 |
S | 490 | F490L | Ttt | Ctt | 5 | 5 | AY.100 | 0.00023 |
S | 490 | F490L | Ttt | Ctt | 5 | 5 | AY.39 | 0.000124 |
S | 490 | F490L | Ttt | Ctt | 5 | 5 | B.1.1.70 | 0.001705 |
S | 490 | F490L | Ttt | Ctt | 5 | 5 | B.1.177.75 | 0.005203 |
S | 490 | F490L | Ttt | Ctt | 4 | 5 | B.1.429 | 0.000094 |
S | 490 | F490L | Ttt | Ctt | 4 | 4 | AY.6 | 0.000165 |
S | 490 | F490L | Ttt | Ctt | 4 | 4 | AY.75 | 0.000224 |
S | 490 | F490L | Ttt | Ctt | 3 | 4 | AY.9.2 | 0.00011 |
S | 490 | F490L | Ttt | Ctt | 3 | 3 | AY.13 | 0.000483 |
S | 490 | F490L | Ttt | Ctt | 3 | 3 | AY.23 | 0.000209 |
S | 490 | F490L | Ttt | Ctt | 3 | 3 | AY.67 | 0.001393 |
S | 490 | F490L | Ttt | Ctt | 3 | 3 | AY.70 | 0.000626 |
S | 490 | F490L | Ttt | Ctt | 2 | 3 | B.1.1.519 | 0.000079 |
S | 490 | F490L | Ttt | Ctt | 2 | 3 | B.1.240 | 0.000431 |
S | 490 | F490L | Ttt | Ctt | 2 | 3 | B.1.526 | 0.000047 |
S | 490 | F490L | Ttt | Ctt | 2 | 3 | P.1 | 0.000032 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | AY.29 | 0.000032 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | AY.30 | 0.000791 |
S | 490 | F490L | Ttt | Ctt | 1 | 2 | AY.33 | 0.000067 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | AY.34.1 | 0.00102 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | AY.54 | 0.000191 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | AY.78 | 0.003082 |
S | 490 | F490L | Ttt | Ctt | 1 | 2 | AY.99 | 0.001049 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | B.1.1.205 | 0.007435 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | B.1.1.216 | 0.001781 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | B.1.1.294 | 0.002532 |
S | 490 | F490L | Ttt | Ctt | 1 | 2 | B.1.351 | 0.00003 |
S | 490 | F490L | Ttt | Ctt | 2 | 2 | B.1.427 | 0.000101 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | A.23.1 | 0.000704 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | A.25 | 0.018182 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AE.8 | 0.000489 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.109 | 0.00074 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.110 | 0.000113 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.113 | 0.000142 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.116 | 0.000287 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.117 | 0.000085 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.12 | 0.000316 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.16 | 0.00038 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.20 | 0.000039 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.24 | 0.000431 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.42 | 0.00004 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.55 | 0.000917 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.59 | 0.00053 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.62 | 0.000436 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.74 | 0.000116 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.84 | 0.000437 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.85 | 0.000427 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.89 | 0.004902 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.9 | 0.000068 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.95 | 0.000761 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | AY.98 | 0.000079 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.1.10 | 0.001115 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.1.214 | 0.000055 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.1.284 | 0.000107 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.1.297 | 0.002237 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.1.351 | 0.002793 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.1.39 | 0.00051 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.1.434 | 0.000349 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.177.20 | 0.001517 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.177.77 | 0.000726 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.177.83 | 0.001481 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.234 | 0.000132 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.236 | 0.002053 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.239 | 0.001221 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.284 | 0.013158 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.356 | 0.001727 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.409 | 0.000781 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.433 | 0.003195 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.596 | 0.000087 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.1.609 | 0.000479 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.3 | 0.000831 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | B.4.5 | 0.011905 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | P.1.14 | 0.000048 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | Q.1 | 0.000126 |
S | 490 | F490L | Ttt | Ctt | 1 | 1 | R.1 | 0.00009 |
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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