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 | 174 | A174A | A354A | syn | gcC | gcT | 1395 | 1338 | 0.95914 | 1325-1327 |
ORF1ab/nsp2 | 174 | A174A | A354A | syn | gcC | gcA | 1395 | 39 | 0.027957 | 1325-1327 |
ORF1ab/nsp2 | 174 | A174A | A354A | syn | gcC | gcG | 1395 | 18 | 0.0129032 | 1325-1327 |
Details of the mutation A174A 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 | 174 | A174A | gcC | gcT | 1338 | 1395 | All | 0.000256 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 39 | 1395 | All | 0.000007 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 18 | 1395 | All | 0.000003 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 905 | 905 | AY.43 | 0.00401 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 50 | 57 | B.1.1.7 | 0.000045 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 4 | 57 | B.1.1.7 | 0.000004 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 3 | 57 | B.1.1.7 | 0.000003 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 34 | 37 | B.1 | 0.000311 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 3 | 37 | B.1 | 0.000027 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 30 | 33 | AY.4 | 0.000047 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 3 | 33 | AY.4 | 0.000005 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 28 | 33 | B.1.617.2 | 0.000105 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 5 | 33 | B.1.617.2 | 0.000019 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 32 | 32 | B.1.1.519 | 0.001271 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 14 | 24 | AY.25 | 0.000084 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 7 | 24 | AY.25 | 0.000042 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 3 | 24 | AY.25 | 0.000018 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 13 | 17 | AY.103 | 0.000081 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 2 | 17 | AY.103 | 0.000012 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 2 | 17 | AY.103 | 0.000012 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 10 | 16 | AY.102 | 0.000265 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 6 | 16 | AY.102 | 0.000159 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 15 | 15 | AY.99.2 | 0.001382 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 15 | 15 | B.1.2 | 0.000132 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 14 | 14 | AY.4.1 | 0.010324 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 10 | 12 | AY.26 | 0.000283 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 2 | 12 | AY.26 | 0.000057 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 11 | 11 | AY.29 | 0.000174 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 10 | 10 | B.1.221 | 0.00071 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 10 | 10 | B.1.429 | 0.000235 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 8 | 8 | P.3 | 0.012759 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 4 | 7 | AY.44 | 0.000024 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 2 | 7 | AY.44 | 0.000012 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 1 | 7 | AY.44 | 0.000006 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 7 | 7 | B.1.1 | 0.000127 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 3 | 6 | AY.39 | 0.000074 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 3 | 6 | AY.39 | 0.000074 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 6 | 6 | B.1.396 | 0.004234 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 5 | 5 | AY.39.1 | 0.000198 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 5 | 5 | AY.54 | 0.000477 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 4 | 5 | P.1 | 0.000063 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 1 | 5 | P.1 | 0.000016 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 4 | 4 | AY.75 | 0.000224 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 4 | 4 | B.1.234 | 0.000528 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 4 | 4 | B.1.427 | 0.000202 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 3 | 3 | AY.113 | 0.000427 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 3 | 3 | AY.20 | 0.000117 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 3 | AY.3 | 0.00002 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 1 | 3 | AY.3 | 0.00001 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 3 | B.1.526 | 0.000047 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcG | 1 | 3 | B.1.526 | 0.000024 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | 0.111111 | |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | AY.100 | 0.000092 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 2 | AY.119 | 0.000035 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 2 | AY.119 | 0.000035 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | AY.3.1 | 0.000171 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | AY.35 | 0.000466 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | AY.47 | 0.000062 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | AY.67 | 0.000929 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | AY.98.1 | 0.000097 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | B.1.164 | 0.029851 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | B.1.351.2 | 0.000605 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | B.1.369 | 0.00057 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | B.1.609 | 0.000959 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 1 | AY.10 | 0.00053 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 1 | AY.16 | 0.00038 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.16.1 | 0.00047 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.30 | 0.000396 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.4.4 | 0.000409 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.46.5 | 0.000198 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.72 | 0.001361 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.73 | 0.000665 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.78 | 0.001541 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.88 | 0.000884 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | AY.93 | 0.000273 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 1 | B | 0.000128 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.1.255 | 0.00303 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.1.317 | 0.000412 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.1.348 | 0.000796 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.1.525 | 0.005464 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.1.61 | 0.008772 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.177.75 | 0.001041 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcA | 1 | 1 | B.1.346 | 0.001311 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.420 | 0.010417 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.576 | 0.000907 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.630 | 0.005236 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | B.1.633 | 0.041667 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | P.1.17 | 0.000162 |
ORF1ab/nsp2 | 174 | A174A | gcC | gcT | 1 | 1 | R.1 | 0.00009 |
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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