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 | 354 | T354I | T3117I | nonsyn | aCt | aTt | 846 | 845 | 0.998818 | 9614-9616 |
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 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 845 | 846 | All | 0.000162 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 229 | 229 | AY.4 | 0.000356 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 56 | 56 | AY.120 | 0.002082 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 56 | 56 | B.1.1.7 | 0.00005 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 47 | 47 | AY.44 | 0.000286 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 35 | 35 | AY.25 | 0.000211 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 35 | 35 | B.1.427 | 0.001767 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 28 | 28 | B.1.617.2 | 0.000105 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 26 | 26 | AY.43 | 0.000115 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 20 | 20 | AY.119 | 0.000706 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 19 | 19 | B.1.2 | 0.000167 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 18 | 18 | B.1 | 0.000165 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 18 | 18 | B.1.1.222 | 0.003672 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 16 | 16 | B.1.234 | 0.002111 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 15 | 15 | AY.103 | 0.000093 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 14 | 14 | AY.4.2 | 0.000304 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 12 | 12 | B.1.1 | 0.000218 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 11 | 11 | AY.3 | 0.000109 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 11 | 11 | AY.39.1 | 0.000436 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 9 | 9 | B.1.429 | 0.000212 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 8 | 8 | AY.29 | 0.000126 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 7 | 7 | B.1.160 | 0.000218 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 6 | 6 | AY.20 | 0.000233 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 6 | 6 | AY.4.5 | 0.000645 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 6 | 6 | AY.5 | 0.000124 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 6 | 6 | AY.98.1 | 0.000291 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 5 | 5 | AY.102 | 0.000133 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 5 | 5 | AY.111 | 0.000916 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 5 | 5 | AY.118 | 0.000313 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 5 | 5 | AY.39 | 0.000124 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 5 | 5 | AY.75 | 0.00028 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 4 | 4 | B.1.621 | 0.000354 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | AY.106 | 0.001005 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | AY.116 | 0.00086 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | AY.24 | 0.001293 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | AY.42 | 0.000121 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | AY.46.6 | 0.000217 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | AY.64 | 0.001786 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | AY.95 | 0.002283 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | B.1.177.60 | 0.000655 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | B.1.177.81 | 0.000568 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 3 | 3 | B.1.517 | 0.001281 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | 0.111111 | |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | AY.7 | 0.000392 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.1.317 | 0.000823 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.177.5 | 0.002484 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.177.86 | 0.000367 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.478 | 0.023529 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.525 | 0.000226 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | B.1.618 | 0.008065 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 2 | 2 | P.2 | 0.000373 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | A.1 | 0.000282 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | A.27 | 0.001656 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B | 0.000128 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.1.262 | 0.015152 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.1.459 | 0.015385 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.128 | 0.000635 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.177.75 | 0.001041 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.214.2 | 0.0006 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.218 | 0.005155 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.351.3 | 0.000876 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.389 | 0.001002 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.413 | 0.004255 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.467 | 0.04 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.1.582 | 0.000491 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.4.5 | 0.011905 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp4 | 354 | T354I | aCt | aTt | 1 | 1 | Q.8 | 0.000165 |
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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