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/nsp4 | 319 | T319I | T3082I | nonsyn | aCt | aTt | 588 | 587 | 0.998299 | 9509-9511 |
ORF1ab/nsp4 | 319 | T319I | T3082I | nonsyn | aCT | aTA | 588 | 1 | 0.00170068 | 9509-9511 |
Details of the mutation T319I 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/nsp4 | 319 | T319I | aCt | aTt | 587 | 588 | All | 0.000112 |
ORF1ab/nsp4 | 319 | T319I | aCT | aTA | 1 | 588 | All | 0 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 164 | 164 | B.1.1.7 | 0.000147 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 46 | 46 | AY.4 | 0.000072 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 46 | 46 | B.1.2 | 0.000405 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 43 | 43 | B.1.526 | 0.001011 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 17 | 17 | AY.103 | 0.000106 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 17 | 17 | AY.34 | 0.001648 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 17 | 17 | B.1.596 | 0.001481 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 14 | 14 | AY.39.1 | 0.000555 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 14 | 14 | B.1.617.2 | 0.000053 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 13 | 13 | AY.25 | 0.000078 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 13 | 13 | AY.27 | 0.000841 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 11 | 11 | AY.39 | 0.000272 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 9 | 9 | AY.43 | 0.00004 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 9 | 9 | B.1 | 0.000082 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 9 | 9 | B.1.177 | 0.000119 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 9 | 9 | B.1.429 | 0.000212 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 8 | 8 | B.1.1 | 0.000145 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 7 | 7 | AY.75 | 0.000392 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 6 | 6 | B.1.1.519 | 0.000238 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 5 | 5 | AY.24 | 0.002155 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 5 | 5 | AY.29 | 0.000079 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 5 | 5 | P.1.17 | 0.000809 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 4 | 4 | AY.102 | 0.000106 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 4 | 4 | AY.44 | 0.000024 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 4 | 4 | AY.99.2 | 0.000369 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 4 | 4 | B.1.1.75 | 0.042553 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 4 | 4 | B.1.160 | 0.000125 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 4 | 4 | B.1.525 | 0.000453 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 3 | 3 | A.27 | 0.004967 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 3 | 3 | AY.16.1 | 0.00141 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 3 | 3 | AY.20 | 0.000117 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 3 | 3 | AY.26 | 0.000085 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 3 | 3 | AY.3 | 0.00003 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 3 | 3 | B.1.612 | 0.007958 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 3 | 3 | P.1 | 0.000047 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | AY.120.2 | 0.002571 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | AY.88 | 0.001768 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | B | 0.000256 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | B.1.1.214 | 0.000111 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | B.1.36.31 | 0.003503 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 2 | 2 | D.2 | 0.00015 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.37 | 0.000316 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.57 | 0.000656 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.58 | 0.000907 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.1.10 | 0.001115 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.1.158 | 0.012195 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.1.187 | 0.00885 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.1.284 | 0.000107 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.1.297 | 0.002237 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.1.326 | 0.001761 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.177.19 | 0.001431 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.206 | 0.000816 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.264 | 0.012346 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.397 | 0.004854 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.459 | 0.004082 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.462 | 0.007246 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.470 | 0.001404 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | C.26 | 0.007353 |
ORF1ab/nsp4 | 319 | T319I | aCT | aTA | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp4 | 319 | T319I | aCt | aTt | 1 | 1 | D.3 | 0.005917 |
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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