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/nsp3 | 543 | S543F | S1361F | nonsyn | tCt | tTt | 934 | 934 | 1 | 4346-4348 |
Details of the mutation S543F 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/nsp3 | 543 | S543F | tCt | tTt | 934 | 934 | All | 0.000179 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 315 | 315 | B.1.1.7 | 0.000282 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 61 | 61 | AY.103 | 0.000379 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 49 | 49 | B.1.617.2 | 0.000185 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 44 | 44 | AY.120 | 0.001636 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 41 | 41 | AY.4 | 0.000064 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 32 | 32 | P.1 | 0.000504 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 24 | 24 | B.1.2 | 0.000211 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 23 | 23 | P.1.7 | 0.007344 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 20 | 20 | AY.43 | 0.000089 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 18 | 18 | AY.8 | 0.010909 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 18 | 18 | B.1.429 | 0.000424 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 17 | 17 | AY.102 | 0.000451 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 15 | 15 | AY.25 | 0.00009 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 15 | 15 | B.1.177.62 | 0.017878 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 15 | 15 | B.1.36.29 | 0.00776 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 13 | 13 | B.1.221 | 0.000923 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 13 | 13 | B.1.525 | 0.001471 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 12 | 12 | AY.4.2 | 0.00026 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 12 | 12 | B.1.177 | 0.000158 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 11 | 11 | P.1.14 | 0.000526 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 9 | 9 | AY.100 | 0.000414 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 9 | 9 | B.1 | 0.000082 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 8 | 8 | B.1.258 | 0.000532 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 7 | 7 | AY.1 | 0.00277 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 7 | 7 | AY.3 | 0.00007 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 7 | 7 | AY.52 | 0.0057 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 7 | 7 | B.1.526 | 0.000165 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 6 | 6 | AY.44 | 0.000037 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 6 | 6 | B.1.1.369 | 0.002677 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 6 | 6 | B.1.258.17 | 0.000624 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 5 | 5 | AY.119 | 0.000177 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 5 | 5 | AY.26 | 0.000142 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 5 | 5 | AY.5 | 0.000103 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 4 | 4 | AY.47 | 0.000124 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 4 | 4 | B.1.351 | 0.000119 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 3 | 3 | AD.2 | 0.000657 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 3 | 3 | AY.4.4 | 0.001227 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 3 | 3 | B.1.311 | 0.000824 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 3 | 3 | B.1.36 | 0.000438 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.10 | 0.00106 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.118 | 0.000125 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.33 | 0.000134 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.41 | 0.000588 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.45 | 0.000243 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.49 | 0.00639 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | AY.7.2 | 0.001119 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | B.1.564 | 0.000852 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 2 | 2 | W.1 | 0.017391 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | A | 0.000387 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | A.1 | 0.000282 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.16.1 | 0.00047 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.58 | 0.000907 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.1.429 | 0.004608 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.1.50 | 0.000679 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.126 | 0.001276 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.214.2 | 0.0006 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.351.2 | 0.000303 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.351.5 | 0.0006 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.361 | 0.001289 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.409 | 0.000781 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.466.1 | 0.007194 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.474 | 0.001901 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.585 | 0.027778 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 543 | S543F | tCt | tTt | 1 | 1 | P.1.10 | 0.000269 |
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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