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 | 409 | R409R | R5733R | syn | cgC | cgT | 1362 | 1312 | 0.963289 | 17461-17463 |
ORF1ab/nsp13 | 409 | R409R | R5733R | syn | cgC | cgA | 1362 | 36 | 0.0264317 | 17461-17463 |
ORF1ab/nsp13 | 409 | R409R | R5733R | syn | cgC | cgG | 1362 | 12 | 0.00881057 | 17461-17463 |
ORF1ab/nsp13 | 409 | R409R | R5733R | syn | CgC | AgA | 1362 | 2 | 0.00146843 | 17461-17463 |
Details of the mutation R409R 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 | 409 | R409R | cgC | cgT | 1312 | 1362 | All | 0.000251 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 36 | 1362 | All | 0.000007 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgG | 12 | 1362 | All | 0.000002 |
ORF1ab/nsp13 | 409 | R409R | CgC | AgA | 2 | 1362 | All | 0 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 556 | 561 | B.1.1.7 | 0.000498 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 5 | 561 | B.1.1.7 | 0.000004 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 114 | 114 | W.1 | 0.991304 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 109 | 110 | AY.4 | 0.00017 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 110 | AY.4 | 0.000002 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 89 | 90 | B.1.617.2 | 0.000335 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 90 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 61 | 63 | B.1.2 | 0.000537 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgG | 1 | 63 | B.1.2 | 0.000009 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 63 | B.1.2 | 0.000009 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 43 | 43 | AY.43 | 0.000191 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 41 | 41 | AY.118 | 0.002569 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 33 | 33 | B.1.427 | 0.001666 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 19 | 32 | AY.25 | 0.000114 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 13 | 32 | AY.25 | 0.000078 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 21 | 26 | B.1 | 0.000192 |
ORF1ab/nsp13 | 409 | R409R | CgC | AgA | 2 | 26 | B.1 | 0.000018 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 2 | 26 | B.1 | 0.000018 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgG | 1 | 26 | B.1 | 0.000009 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 20 | 20 | B.1.621 | 0.00177 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 14 | 14 | AY.30 | 0.00554 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 13 | 13 | AY.39 | 0.000321 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 11 | 12 | AY.103 | 0.000068 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 12 | AY.103 | 0.000006 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 10 | 10 | AY.102 | 0.000265 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 10 | 10 | B.1.1 | 0.000181 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgG | 6 | 10 | P.1 | 0.000095 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 4 | 10 | P.1 | 0.000063 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 8 | 8 | AY.44 | 0.000049 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 8 | 8 | B.1.526 | 0.000188 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 7 | 7 | AY.20 | 0.000272 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 7 | 7 | B.1.177 | 0.000092 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 5 | 6 | A.2.5 | 0.002495 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 6 | A.2.5 | 0.000499 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 6 | 6 | AY.116 | 0.001721 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 5 | 6 | AY.3 | 0.00005 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 6 | AY.3 | 0.00001 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 6 | 6 | B.1.351 | 0.000178 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 6 | 6 | B.1.36.29 | 0.003104 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 4 | 4 | B.1.177.16 | 0.002658 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgG | 4 | 4 | B.1.236 | 0.008214 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 4 | 4 | B.1.258 | 0.000266 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 4 | 4 | B.1.433 | 0.01278 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | AY.40 | 0.002893 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | AY.5 | 0.000062 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | AY.54 | 0.000286 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | AY.9.1 | 0.000251 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | B.1.160 | 0.000094 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | B.1.177.62 | 0.003576 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | P.1.15 | 0.000697 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 3 | 3 | P.1.7 | 0.000958 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | AY.24 | 0.000862 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | AY.46 | 0.000208 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | AY.98 | 0.000158 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | B.1.1.28 | 0.000622 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 2 | B.1.177.60 | 0.000218 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 2 | B.1.177.60 | 0.000218 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | B.1.606 | 0.012048 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 2 | 2 | Q.1 | 0.000253 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.49 | 0.003195 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.53 | 0.000288 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.62 | 0.000436 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgA | 1 | 1 | AY.69 | 0.000187 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.90 | 0.000684 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.1.1 | 0.000327 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.1.170 | 0.001247 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.1.231 | 0.003096 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.160.16 | 0.000929 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.160.20 | 0.008929 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.177.83 | 0.001481 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.195 | 0.005025 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.324 | 0.001605 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.36.18 | 0.00042 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.497 | 0.000315 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.623 | 0.000536 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | C.16 | 0.00106 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | P.3 | 0.001595 |
ORF1ab/nsp13 | 409 | R409R | cgC | cgT | 1 | 1 | Q.3 | 0.000145 |
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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