CoV-GLUE | Mutations | Mutation
CoV-GLUE Mutation: ORF = ORF1ab/nsp1 : Mut = S3R
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/nsp1 | 3 | S3R | S3R | nonsyn | Agc | Cgc | 73 | 38 | 0.520548 | 272-274 |
| ORF1ab/nsp1 | 3 | S3R | S3R | nonsyn | agC | agA | 73 | 33 | 0.452055 | 272-274 |
| ORF1ab/nsp1 | 3 | S3R | S3R | nonsyn | agC | agG | 73 | 2 | 0.0273973 | 272-274 |
Details of the mutation S3R 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/nsp1 | 3 | S3R | Agc | Cgc | 38 | 73 | All | 0.000007 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 33 | 73 | All | 0.000006 |
| ORF1ab/nsp1 | 3 | S3R | agC | agG | 2 | 73 | All | 0 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 25 | 30 | B.1.1.7 | 0.000022 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 5 | 30 | B.1.1.7 | 0.000004 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 4 | 5 | AY.25 | 0.000024 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 5 | AY.25 | 0.000006 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 4 | 4 | AY.22 | 0.008368 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 3 | 3 | B.1.2 | 0.000026 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 2 | 3 | B.1.617.2 | 0.000008 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 3 | B.1.617.2 | 0.000004 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 2 | 2 | AY.4 | 0.000003 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 2 | B.1 | 0.000009 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 2 | B.1 | 0.000009 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 2 | 2 | B.1.37 | 0.029412 |
| ORF1ab/nsp1 | 3 | S3R | agC | agG | 1 | 1 | 0.055556 | |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | A | 0.000387 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | AY.103 | 0.000006 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.114 | 0.000231 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.118 | 0.000063 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | AY.23 | 0.00007 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.3 | 0.00001 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.43 | 0.000004 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.44 | 0.000006 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | AY.45 | 0.000122 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.50 | 0.000799 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.6 | 0.000041 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | AY.62 | 0.000436 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | AY.9.1 | 0.000084 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | AY.99 | 0.001049 |
| ORF1ab/nsp1 | 3 | S3R | agC | agG | 1 | 1 | B.1.1 | 0.000018 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | B.1.177 | 0.000013 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | B.1.240 | 0.000216 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | B.1.258 | 0.000067 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | B.1.538 | 0.008065 |
| ORF1ab/nsp1 | 3 | S3R | Agc | Cgc | 1 | 1 | B.1.617.1 | 0.000129 |
| ORF1ab/nsp1 | 3 | S3R | agC | agA | 1 | 1 | P.1 | 0.000016 |
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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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