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/nsp13 | 301 | S301S | S5625S | syn | tcT | tcA | 2364 | 2063 | 0.872673 | 17137-17139 |
ORF1ab/nsp13 | 301 | S301S | S5625S | syn | tcT | tcC | 2364 | 266 | 0.112521 | 17137-17139 |
ORF1ab/nsp13 | 301 | S301S | S5625S | syn | tcT | tcG | 2364 | 24 | 0.0101523 | 17137-17139 |
ORF1ab/nsp13 | 301 | S301S | S5625S | syn | TCT | AGC | 2364 | 6 | 0.00253807 | 17137-17139 |
ORF1ab/nsp13 | 301 | S301S | S5625S | syn | TCt | AGt | 2364 | 5 | 0.00211506 | 17137-17139 |
Details of the mutation S301S 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/nsp13 | 301 | S301S | tcT | tcA | 2063 | 2364 | All | 0.000395 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 266 | 2364 | All | 0.000051 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 24 | 2364 | All | 0.000005 |
ORF1ab/nsp13 | 301 | S301S | TCT | AGC | 6 | 2364 | All | 0.000001 |
ORF1ab/nsp13 | 301 | S301S | TCt | AGt | 5 | 2364 | All | 0.000001 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1774 | 1848 | B.1.1.7 | 0.001588 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 53 | 1848 | B.1.1.7 | 0.000047 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 10 | 1848 | B.1.1.7 | 0.000009 |
ORF1ab/nsp13 | 301 | S301S | TCT | AGC | 6 | 1848 | B.1.1.7 | 0.000005 |
ORF1ab/nsp13 | 301 | S301S | TCt | AGt | 5 | 1848 | B.1.1.7 | 0.000004 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 48 | 79 | AY.4 | 0.000075 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 31 | 79 | AY.4 | 0.000048 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 53 | 53 | AU.3 | 0.111814 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 42 | 42 | AY.14 | 0.003697 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 17 | 35 | B.1.617.2 | 0.000064 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 15 | 35 | B.1.617.2 | 0.000056 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 3 | 35 | B.1.617.2 | 0.000011 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 27 | 27 | B.1.1.50 | 0.01833 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 23 | 23 | AY.68 | 0.006296 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 15 | 18 | AY.39 | 0.000371 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 3 | 18 | AY.39 | 0.000074 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 15 | 15 | B.1.1.348 | 0.011943 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 11 | 15 | R.1 | 0.00099 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 4 | 15 | R.1 | 0.00036 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 14 | 14 | B.4.8 | 1 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 8 | 12 | AY.43 | 0.000035 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 4 | 12 | AY.43 | 0.000018 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 7 | 10 | AY.102 | 0.000186 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 2 | 10 | AY.102 | 0.000053 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 10 | AY.102 | 0.000027 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 6 | 10 | AY.26 | 0.00017 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 4 | 10 | AY.26 | 0.000113 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 9 | 10 | B.1 | 0.000082 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 10 | B.1 | 0.000009 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 5 | 8 | AY.3 | 0.00005 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 2 | 8 | AY.3 | 0.00002 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 8 | AY.3 | 0.00001 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 6 | 7 | B.1.1 | 0.000109 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 7 | B.1.1 | 0.000018 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 7 | 7 | B.1.1.263 | 0.010903 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 4 | 7 | P.1 | 0.000063 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 3 | 7 | P.1 | 0.000047 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 6 | 7 | P.1.14 | 0.000287 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 7 | P.1.14 | 0.000048 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 4 | 6 | B.1.2 | 0.000035 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 2 | 6 | B.1.2 | 0.000018 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 5 | 6 | B.1.429 | 0.000118 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 6 | B.1.429 | 0.000024 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 4 | 5 | B.1.177 | 0.000053 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 5 | B.1.177 | 0.000013 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 4 | 4 | AY.39.1 | 0.000158 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 3 | 4 | B.1.526 | 0.000071 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 4 | B.1.526 | 0.000024 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 3 | 3 | AY.100 | 0.000138 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 3 | 3 | AY.42 | 0.000121 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 2 | 3 | AY.44 | 0.000012 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 3 | AY.44 | 0.000006 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 2 | 3 | AY.98 | 0.000158 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 3 | AY.98 | 0.000079 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 3 | 3 | B | 0.000383 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 3 | 3 | B.1.1.519 | 0.000119 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 3 | 3 | B.1.221.3 | 0.0025 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 3 | 3 | B.1.628 | 0.001057 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 3 | 3 | C.36 | 0.002732 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 2 | AY.25 | 0.000006 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 2 | AY.25 | 0.000006 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 2 | 2 | AY.5.4 | 0.000553 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 2 | AY.54 | 0.000095 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 2 | AY.54 | 0.000095 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 2 | 2 | B.1.471 | 0.005464 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 2 | 2 | B.1.595 | 0.000522 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 2 | 2 | B.1.596 | 0.000174 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 2 | 2 | Q.2 | 0.001227 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | A | 0.000387 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.40 | 0.000964 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.69 | 0.000187 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 1 | 1 | AY.73 | 0.000665 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | AY.87 | 0.000833 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.1.189 | 0.001513 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcG | 1 | 1 | B.1.1.277 | 0.000759 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.1.298 | 0.000862 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.157 | 0.002985 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.177.5 | 0.001242 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.177.54 | 0.000606 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.215 | 0.009615 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.223 | 0.002778 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.258.5 | 0.008772 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.340 | 0.004292 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.361 | 0.001289 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.398 | 0.002976 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.520 | 0.021739 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.587 | 0.001898 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.4 | 0.002208 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.4.7 | 0.010101 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | B.58 | 0.010204 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcC | 1 | 1 | P.1.2 | 0.001156 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp13 | 301 | S301S | tcT | tcA | 1 | 1 | Q.8 | 0.000165 |
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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