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 | 325 | S325S | S3088S | syn | tcA | tcG | 5727 | 5680 | 0.991793 | 9527-9529 |
ORF1ab/nsp4 | 325 | S325S | S3088S | syn | tcA | tcT | 5727 | 38 | 0.00663524 | 9527-9529 |
ORF1ab/nsp4 | 325 | S325S | S3088S | syn | tcA | tcC | 5727 | 9 | 0.0015715 | 9527-9529 |
Details of the mutation S325S 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 | 325 | S325S | tcA | tcG | 5680 | 5727 | All | 0.001086 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 38 | 5727 | All | 0.000007 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcC | 9 | 5727 | All | 0.000002 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 5051 | 5051 | Q.3 | 0.73256 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 127 | 129 | B.1.177 | 0.001672 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 2 | 129 | B.1.177 | 0.000026 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 94 | 96 | B.1.617.2 | 0.000354 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 2 | 96 | B.1.617.2 | 0.000008 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 82 | 87 | B.1.1.7 | 0.000073 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 5 | 87 | B.1.1.7 | 0.000004 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 45 | 45 | AY.20 | 0.001749 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 43 | 43 | AY.98.1 | 0.002083 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 33 | 36 | AY.4 | 0.000051 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 3 | 36 | AY.4 | 0.000005 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 34 | 34 | B.1.619 | 0.029617 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 21 | 24 | AY.25 | 0.000126 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcC | 2 | 24 | AY.25 | 0.000012 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 24 | AY.25 | 0.000006 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 10 | 18 | AY.29 | 0.000158 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 8 | 18 | AY.29 | 0.000126 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 11 | 16 | B.1.2 | 0.000097 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcC | 4 | 16 | B.1.2 | 0.000035 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 16 | B.1.2 | 0.000009 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 11 | 14 | AY.102 | 0.000292 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 3 | 14 | AY.102 | 0.00008 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 12 | 12 | AY.43 | 0.000053 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 9 | 12 | B.1 | 0.000082 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 2 | 12 | B.1 | 0.000018 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcC | 1 | 12 | B.1 | 0.000009 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 8 | 9 | AY.103 | 0.00005 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcC | 1 | 9 | AY.103 | 0.000006 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 6 | 9 | AY.26 | 0.00017 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 3 | 9 | AY.26 | 0.000085 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 7 | 8 | B.1.1 | 0.000127 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 8 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 6 | 6 | P.1 | 0.000095 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 5 | 5 | AY.44 | 0.00003 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 3 | 3 | AY.3 | 0.00003 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 3 | 3 | AY.9 | 0.000203 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 3 | 3 | AY.98 | 0.000237 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 3 | B.1.160 | 0.000062 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcC | 1 | 3 | B.1.160 | 0.000031 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 3 | 3 | B.1.576 | 0.00272 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 3 | D.2 | 0.00015 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 3 | D.2 | 0.000075 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 3 | 3 | Q.8 | 0.000495 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 2 | AY.108 | 0.002205 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 2 | AY.46 | 0.000208 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 2 | AY.5 | 0.000021 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 2 | AY.54 | 0.000191 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 2 | AY.75.1 | 0.000361 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 2 | B.1.206 | 0.001631 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 2 | 2 | C.1 | 0.004785 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 1 | AY.14 | 0.000088 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.69 | 0.000187 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B | 0.000128 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.1.524 | 0.020833 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.126 | 0.001276 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.146 | 0.004237 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.177.46 | 0.000918 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcT | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.452 | 0.013699 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | P.1.16 | 0.000374 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | Q.4 | 0.000455 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | R.1 | 0.00009 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | W.1 | 0.008696 |
ORF1ab/nsp4 | 325 | S325S | tcA | tcG | 1 | 1 | W.3 | 0.005263 |
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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