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/nsp3 | 550 | L550L | L1368L | syn | ctT | ctC | 804 | 556 | 0.691542 | 4367-4369 |
ORF1ab/nsp3 | 550 | L550L | L1368L | syn | ctT | ctA | 804 | 222 | 0.276119 | 4367-4369 |
ORF1ab/nsp3 | 550 | L550L | L1368L | syn | ctT | ctG | 804 | 16 | 0.0199005 | 4367-4369 |
ORF1ab/nsp3 | 550 | L550L | L1368L | syn | CtT | TtG | 804 | 9 | 0.011194 | 4367-4369 |
ORF1ab/nsp3 | 550 | L550L | L1368L | syn | CtT | TtA | 804 | 1 | 0.00124378 | 4367-4369 |
Details of the mutation L550L 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/nsp3 | 550 | L550L | ctT | ctC | 556 | 804 | All | 0.000106 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 222 | 804 | All | 0.000042 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 16 | 804 | All | 0.000003 |
ORF1ab/nsp3 | 550 | L550L | CtT | TtG | 9 | 804 | All | 0.000002 |
ORF1ab/nsp3 | 550 | L550L | CtT | TtA | 1 | 804 | All | 0 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 323 | 323 | B.1.1.280 | 0.996914 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 95 | 104 | AY.103 | 0.00059 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 9 | 104 | AY.103 | 0.000056 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 67 | 71 | AY.43 | 0.000297 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 2 | 71 | AY.43 | 0.000009 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 2 | 71 | AY.43 | 0.000009 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 56 | 60 | AY.3 | 0.000557 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 4 | 60 | AY.3 | 0.00004 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 56 | 56 | AY.111 | 0.010256 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 22 | 24 | B.1 | 0.000202 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 24 | B.1 | 0.000009 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 24 | B.1 | 0.000009 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 9 | 16 | B.1.1.7 | 0.000008 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 6 | 16 | B.1.1.7 | 0.000005 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 16 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 9 | 14 | AY.4 | 0.000014 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 5 | 14 | AY.4 | 0.000008 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 13 | 13 | AY.5.4 | 0.003597 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 7 | 7 | AY.119 | 0.000247 |
ORF1ab/nsp3 | 550 | L550L | CtT | TtG | 7 | 7 | AY.14 | 0.000616 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 2 | 6 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 2 | 6 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 2 | 6 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 5 | 5 | AD.2 | 0.001095 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 5 | 5 | AY.61 | 0.000524 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 4 | 5 | B.1.2 | 0.000035 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 5 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 5 | 5 | B.1.575 | 0.001517 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 3 | 4 | AY.33 | 0.0002 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 4 | AY.33 | 0.000067 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 3 | 4 | AY.35 | 0.000699 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 4 | AY.35 | 0.000233 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 4 | 4 | B.1.177.81 | 0.000757 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 4 | 4 | B.1.375 | 0.003279 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 3 | 3 | B.1.160 | 0.000094 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 3 | 3 | B.1.36 | 0.000438 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 3 | 3 | B.1.470 | 0.004213 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 3 | 3 | B.1.617.2 | 0.000011 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 2 | 3 | C.37 | 0.000232 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 3 | C.37 | 0.000116 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 2 | 2 | AY.24 | 0.000862 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 2 | AY.27 | 0.000065 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 2 | AY.27 | 0.000065 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 2 | 2 | AY.37 | 0.000632 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 2 | 2 | AY.44 | 0.000012 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 2 | AY.46.6 | 0.000072 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 2 | AY.46.6 | 0.000072 |
ORF1ab/nsp3 | 550 | L550L | CtT | TtG | 1 | 2 | AY.54 | 0.000095 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 2 | AY.54 | 0.000095 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 2 | 2 | B.1.1.326 | 0.003521 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 2 | 2 | B.1.1.33 | 0.000842 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp3 | 550 | L550L | CtT | TtG | 1 | 2 | B.1.258.17 | 0.000104 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 2 | B.1.258.17 | 0.000104 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 2 | 2 | B.1.466.2 | 0.000782 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 2 | 2 | C.36 | 0.001821 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | AU.2 | 0.002421 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | AY.16 | 0.00038 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | AY.66 | 0.00107 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | AY.7 | 0.000196 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 1 | B.1.1.174 | 0.003378 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | B.1.1.63 | 0.000386 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | B.1.177.6 | 0.000977 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | B.1.177.86 | 0.000183 |
ORF1ab/nsp3 | 550 | L550L | CtT | TtA | 1 | 1 | B.1.237 | 0.004975 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | B.6.6 | 0.000889 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctG | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 550 | L550L | ctT | ctA | 1 | 1 | Q.3 | 0.000145 |
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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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