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/nsp5A-B | 131 | R131R | R3394R | syn | agG | agA | 1150 | 1056 | 0.918261 | 10445-10447 |
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/nsp5A-B | 131 | R131R | agG | agA | 1056 | 1150 | All | 0.000202 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 283 | 284 | AY.103 | 0.001757 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 170 | 170 | B.1.1.222 | 0.03468 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 89 | 90 | AY.4 | 0.000139 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 87 | 89 | B.1.1.7 | 0.000078 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 63 | 64 | B.1.617.2 | 0.000237 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 53 | 53 | A.15 | 0.84127 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 42 | 42 | P.1.14 | 0.002008 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 30 | B.1.243 | 0.00007 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 4 | 29 | AY.29 | 0.000063 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 29 | 29 | AY.5 | 0.000599 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 20 | 21 | B.1.2 | 0.000176 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 10 | 20 | AY.44 | 0.000061 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 20 | 20 | B.1.609 | 0.009588 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 16 | 17 | AY.43 | 0.000071 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 13 | 13 | B.1 | 0.000119 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 11 | 13 | B.1.1 | 0.0002 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 8 | 11 | B.1.177 | 0.000105 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 11 | 11 | B.1.240 | 0.002371 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 10 | 10 | AY.25 | 0.00006 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 8 | 8 | AY.26 | 0.000226 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 6 | 6 | B.1.1.519 | 0.000238 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 5 | 5 | B.1.596 | 0.000436 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 4 | 4 | AY.100 | 0.000184 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 4 | 4 | AY.75 | 0.000224 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 4 | 4 | AY.86 | 0.00332 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 4 | 4 | B.1.1.269 | 0.005413 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 4 | 4 | P.1 | 0.000063 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 3 | 3 | AY.102 | 0.00008 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 3 | AY.20 | 0.000078 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 3 | 3 | AY.27 | 0.000194 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 3 | 3 | AY.3.1 | 0.000256 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 3 | 3 | AY.58 | 0.002722 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 3 | 3 | AY.6 | 0.000123 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 3 | 3 | C.37 | 0.000348 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 2 | AY.117 | 0.000169 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 2 | AY.14 | 0.000176 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 2 | AY.3 | 0.00001 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 2 | AY.39.1 | 0.00004 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 2 | B.1.177.10 | 0.001756 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | A.21 | 0.00277 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | A.23.1 | 0.000704 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | A.5 | 0.001923 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AE.8 | 0.000489 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.10 | 0.00053 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.105 | 0.000643 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.4.3 | 0.000842 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | AY.7 | 0.000196 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B | 0.000128 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.1.28 | 0.000311 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.1.291 | 0.000742 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.1.301 | 0.001179 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.1.500 | 0.02 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.149 | 0.003425 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.210 | 0.002132 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.232 | 0.000537 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.36.12 | 0.009615 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.560 | 0.00463 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.620 | 0.000946 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp5A-B | 131 | R131R | agG | agA | 1 | 1 | P.1.16 | 0.000374 |
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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