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/nsp2 | 380 | R380R | R560R | syn | cgT | cgC | 796 | 559 | 0.702261 | 1943-1945 |
ORF1ab/nsp2 | 380 | R380R | R560R | syn | cgT | cgG | 796 | 149 | 0.187186 | 1943-1945 |
ORF1ab/nsp2 | 380 | R380R | R560R | syn | cgT | cgA | 796 | 69 | 0.0866834 | 1943-1945 |
ORF1ab/nsp2 | 380 | R380R | R560R | syn | CgT | AgA | 796 | 11 | 0.0138191 | 1943-1945 |
ORF1ab/nsp2 | 380 | R380R | R560R | syn | CgT | AgG | 796 | 8 | 0.0100503 | 1943-1945 |
Details of the mutation R380R 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/nsp2 | 380 | R380R | cgT | cgC | 559 | 796 | All | 0.000107 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 149 | 796 | All | 0.000028 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 69 | 796 | All | 0.000013 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgA | 11 | 796 | All | 0.000002 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgG | 8 | 796 | All | 0.000002 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 237 | 237 | AY.4.2 | 0.00514 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 89 | 94 | AY.44 | 0.000542 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 5 | 94 | AY.44 | 0.00003 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 75 | 76 | AY.4 | 0.000117 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 76 | AY.4 | 0.000002 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 45 | 59 | B.1.1.7 | 0.00004 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgA | 8 | 59 | B.1.1.7 | 0.000007 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgG | 3 | 59 | B.1.1.7 | 0.000003 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 2 | 59 | B.1.1.7 | 0.000002 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 59 | B.1.1.7 | 0.000001 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 51 | 54 | AY.103 | 0.000317 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 3 | 54 | AY.103 | 0.000019 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 17 | 39 | B.1 | 0.000156 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 11 | 39 | B.1 | 0.000101 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 8 | 39 | B.1 | 0.000073 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgG | 2 | 39 | B.1 | 0.000018 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgA | 1 | 39 | B.1 | 0.000009 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 34 | 36 | B.1.258 | 0.002263 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 36 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgG | 1 | 36 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 29 | 30 | AY.43 | 0.000128 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 30 | AY.43 | 0.000004 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 19 | 21 | B.1.617.2 | 0.000072 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 21 | B.1.617.2 | 0.000004 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 21 | B.1.617.2 | 0.000004 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 18 | 18 | AY.3.1 | 0.001535 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 15 | 15 | AY.3 | 0.000149 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 13 | 13 | AY.106 | 0.004354 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 9 | 9 | B.1.1.28 | 0.002801 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 8 | 8 | B.1.2 | 0.00007 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 4 | 7 | B.1.1 | 0.000073 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 2 | 7 | B.1.1 | 0.000036 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 7 | B.1.1 | 0.000018 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 4 | 5 | AY.26 | 0.000113 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 5 | AY.26 | 0.000028 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 5 | 5 | AY.45 | 0.000608 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgG | 1 | 5 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgA | 1 | 5 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 5 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 5 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 5 | B.1.177 | 0.000013 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 5 | 5 | B.1.36 | 0.00073 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 4 | 5 | D.2 | 0.0003 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 5 | D.2 | 0.000075 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 4 | 4 | AY.119 | 0.000141 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgG | 1 | 4 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 380 | R380R | CgT | AgA | 1 | 4 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 4 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 4 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 4 | 4 | P.1 | 0.000063 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 3 | 3 | AY.75 | 0.000168 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 3 | 3 | B.1.429 | 0.000071 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 2 | B.1.1.1 | 0.000327 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 2 | B.1.1.1 | 0.000327 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 2 | 2 | B.1.177.57 | 0.000562 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 2 | 2 | B.1.222 | 0.003384 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 2 | 2 | B.1.526 | 0.000047 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 2 | B.1.609 | 0.000479 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 2 | B.1.609 | 0.000479 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | AY.16 | 0.00038 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | AY.34.1 | 0.00051 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | B.1.1.122 | 0.045455 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 1 | B.1.1.170 | 0.001247 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | B.1.1.354 | 0.004386 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | B.1.160.7 | 0.002079 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 1 | B.1.177.11 | 0.001698 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgA | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp2 | 380 | R380R | cgT | cgG | 1 | 1 | B.23 | 0.002924 |
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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