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 | 1578 | S1578I | S2396I | nonsyn | aGt | aTt | 4514 | 4514 | 1 | 7451-7453 |
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/nsp3 | 1578 | S1578I | aGt | aTt | 4514 | 4514 | All | 0.000863 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1653 | 1653 | B.1.1.317 | 0.680527 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1434 | 1434 | AY.3 | 0.014263 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 285 | 285 | B.1.617.2 | 0.001073 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 122 | 122 | AY.105 | 0.078457 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 118 | 118 | AY.42 | 0.004747 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 106 | 106 | B.1.1.7 | 0.000095 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 101 | 101 | AY.102 | 0.002678 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 79 | 79 | AY.25 | 0.000475 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 64 | 64 | AS.2 | 1 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 54 | 54 | AY.116 | 0.015486 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 51 | 51 | AY.4 | 0.000079 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 48 | 48 | B.1.1 | 0.000871 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 46 | 46 | B.1 | 0.000421 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 29 | 29 | AY.39 | 0.000717 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 27 | 27 | B.1.595 | 0.007046 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 20 | 20 | AY.43 | 0.000089 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 19 | 19 | AY.68 | 0.005201 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 19 | 19 | AY.85 | 0.008116 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 18 | 18 | B.1.1.189 | 0.027231 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 17 | 17 | AY.44 | 0.000103 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 17 | 17 | B.1.633 | 0.708333 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 15 | 15 | P.1 | 0.000236 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 13 | 13 | AY.103 | 0.000081 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 13 | 13 | AY.117 | 0.001099 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 9 | 9 | AY.46.2 | 0.005718 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 9 | 9 | AY.91 | 0.006574 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 9 | 9 | B.1.2 | 0.000079 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 8 | 8 | AY.63 | 0.003095 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 7 | 7 | AY.46 | 0.000729 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 6 | 6 | B.1.139 | 0.004399 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 5 | 5 | AY.120 | 0.000186 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 5 | 5 | AY.5.3 | 0.001687 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 5 | 5 | B.1.1.277 | 0.003794 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 4 | 4 | AY.26 | 0.000113 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 4 | 4 | B.1.1.253 | 0.010025 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 4 | 4 | B.1.1.26 | 0.020942 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 3 | 3 | AY.45 | 0.000365 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 3 | 3 | AY.75 | 0.000168 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 3 | 3 | AY.75.1 | 0.000541 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 3 | 3 | B.1.110 | 0.013575 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 3 | 3 | B.1.346 | 0.003932 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 3 | 3 | B.1.400 | 0.001287 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 3 | 3 | P.1.14 | 0.000143 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | AY.118 | 0.000125 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | AY.36 | 0.000296 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | AY.37 | 0.000632 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | AY.5 | 0.000041 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | AY.9.1 | 0.000167 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | AY.92 | 0.000575 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | B.1.1.33 | 0.000842 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | B.1.1.370 | 0.025316 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | B.1.1.521 | 0.010695 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.88 | 0.000884 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.94 | 0.000443 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | AY.95 | 0.000761 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B | 0.000128 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.1.10 | 0.001115 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.1.198 | 0.001468 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.1.336 | 0.016667 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.1.389 | 0.006061 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.177.77 | 0.000726 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.470 | 0.001404 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.558 | 0.004566 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 1578 | S1578I | aGt | aTt | 1 | 1 | P.1.12 | 0.000484 |
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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