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 | 109 | P109S | P927S | nonsyn | Cca | Tca | 554 | 551 | 0.994585 | 3044-3046 |
ORF1ab/nsp3 | 109 | P109S | P927S | nonsyn | CcA | TcT | 554 | 2 | 0.00361011 | 3044-3046 |
ORF1ab/nsp3 | 109 | P109S | P927S | nonsyn | CcA | TcC | 554 | 1 | 0.00180505 | 3044-3046 |
Details of the mutation P109S 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 | 109 | P109S | Cca | Tca | 551 | 554 | All | 0.000105 |
ORF1ab/nsp3 | 109 | P109S | CcA | TcT | 2 | 554 | All | 0 |
ORF1ab/nsp3 | 109 | P109S | CcA | TcC | 1 | 554 | All | 0 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 112 | 112 | B.1.1.7 | 0.0001 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 107 | 107 | AY.103 | 0.000664 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 34 | 34 | AY.4 | 0.000053 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 30 | 30 | B.1.617.2 | 0.000113 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 23 | 23 | AY.3 | 0.000229 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 23 | 23 | AY.5 | 0.000475 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 19 | 19 | AY.118 | 0.00119 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 11 | 11 | AY.100 | 0.000506 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 11 | 11 | AY.111 | 0.002015 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 11 | 11 | AY.44 | 0.000067 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 9 | 10 | D.2 | 0.000675 |
ORF1ab/nsp3 | 109 | P109S | CcA | TcT | 1 | 10 | D.2 | 0.000075 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 8 | 8 | AY.43 | 0.000035 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 8 | 8 | B.1.1.369 | 0.00357 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 8 | 8 | B.1.2 | 0.00007 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 6 | 6 | AY.23 | 0.000418 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 5 | 5 | AY.119 | 0.000177 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 5 | 5 | AY.75 | 0.00028 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 5 | 5 | B.1.1.374 | 0.011876 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 5 | 5 | B.1.221 | 0.000355 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 5 | 5 | P.1 | 0.000079 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 4 | 4 | AY.102 | 0.000106 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 4 | 4 | AY.15 | 0.008889 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 4 | 4 | B.1.1.71 | 0.024242 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | A | 0.001161 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 3 | AY.105 | 0.001286 |
ORF1ab/nsp3 | 109 | P109S | CcA | TcT | 1 | 3 | AY.105 | 0.000643 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | AY.14 | 0.000264 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | AY.25 | 0.000018 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | AY.48 | 0.001395 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | AY.98 | 0.000237 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | B.1.36 | 0.000438 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | B.1.596 | 0.000261 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | B.1.617.1 | 0.000387 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 3 | 3 | C.37 | 0.000348 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | AY.117 | 0.000169 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | AY.73 | 0.001331 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.1.411 | 0.029412 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.243 | 0.000139 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 2 | 2 | B.1.436 | 0.002058 |
ORF1ab/nsp3 | 109 | P109S | CcA | TcC | 1 | 1 | AY.109 | 0.00074 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.37 | 0.000316 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.4.4 | 0.000409 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.50 | 0.000799 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | AY.79 | 0.001211 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.1.216 | 0.00089 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.1.344 | 0.010753 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.1.389 | 0.006061 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.1.434 | 0.000349 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.1.506 | 0.037037 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.177.17 | 0.000821 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.177.44 | 0.000519 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.177.5 | 0.001242 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.177.65 | 0.000665 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.328 | 0.03125 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.375 | 0.00082 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.38 | 0.032258 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.426 | 0.001009 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | B.1.565 | 0.00081 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | P.7 | 0.004367 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | Q.8 | 0.000165 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | R.1 | 0.00009 |
ORF1ab/nsp3 | 109 | P109S | Cca | Tca | 1 | 1 | U.3 | 0.003861 |
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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