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/nsp1 | 4 | L4L | L4L | syn | ctT | ctC | 1718 | 1430 | 0.832363 | 275-277 |
ORF1ab/nsp1 | 4 | L4L | L4L | syn | ctT | ctA | 1718 | 267 | 0.155413 | 275-277 |
ORF1ab/nsp1 | 4 | L4L | L4L | syn | ctT | ctG | 1718 | 21 | 0.0122235 | 275-277 |
Details of the mutation L4L 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/nsp1 | 4 | L4L | ctT | ctC | 1430 | 1718 | All | 0.000274 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 267 | 1718 | All | 0.000051 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 21 | 1718 | All | 0.000004 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 957 | 1003 | B.1.1.7 | 0.000857 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 40 | 1003 | B.1.1.7 | 0.000036 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 6 | 1003 | B.1.1.7 | 0.000005 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 245 | 245 | B.1.1.519 | 0.009729 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 100 | 100 | B.1.525 | 0.011316 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 52 | 54 | B.1.526 | 0.001222 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 54 | B.1.526 | 0.000047 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 35 | 36 | Q.1 | 0.004421 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 36 | Q.1 | 0.000126 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 15 | 28 | AY.4 | 0.000023 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 12 | 28 | AY.4 | 0.000019 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 28 | AY.4 | 0.000002 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 12 | 22 | AY.26 | 0.00034 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 10 | 22 | AY.26 | 0.000283 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 17 | 21 | AY.103 | 0.000106 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 4 | 21 | AY.103 | 0.000025 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 14 | 19 | B.1.617.2 | 0.000053 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 4 | 19 | B.1.617.2 | 0.000015 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 19 | B.1.617.2 | 0.000004 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 13 | 15 | B.1 | 0.000119 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 15 | B.1 | 0.000018 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 10 | 12 | AY.25 | 0.00006 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 12 | AY.25 | 0.000012 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 9 | 10 | AY.44 | 0.000055 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 10 | AY.44 | 0.000006 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 6 | 9 | AY.43 | 0.000027 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 3 | 9 | AY.43 | 0.000013 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 6 | 9 | B.1.1 | 0.000109 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 9 | B.1.1 | 0.000036 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 9 | B.1.1 | 0.000018 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 4 | 9 | P.1 | 0.000063 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 3 | 9 | P.1 | 0.000047 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 9 | P.1 | 0.000032 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 7 | 8 | AY.119 | 0.000247 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 8 | AY.119 | 0.000035 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 5 | 6 | AY.39.1 | 0.000198 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 6 | AY.39.1 | 0.00004 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 6 | 6 | B.1.324 | 0.009631 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 3 | 5 | AY.3 | 0.00003 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 5 | AY.3 | 0.00001 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 5 | AY.3 | 0.00001 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 4 | 5 | B.1.2 | 0.000035 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 5 | B.1.2 | 0.000009 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 3 | 4 | AY.113 | 0.000427 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 4 | AY.113 | 0.000142 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 4 | 4 | B.1.1.486 | 0.006309 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 4 | B.1.177 | 0.000026 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 4 | B.1.177 | 0.000026 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 3 | AY.102 | 0.000053 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 3 | AY.102 | 0.000027 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 3 | AY.118 | 0.000125 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 3 | AY.118 | 0.000063 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 3 | AY.46 | 0.000208 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 3 | AY.46 | 0.000104 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 3 | 3 | AY.47 | 0.000093 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 3 | 3 | B.1.128 | 0.001906 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 3 | 3 | B.1.639 | 0.065217 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 3 | 3 | R.1 | 0.00027 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 2 | AY.101 | 0.000981 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | AY.29.1 | 0.000441 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | AY.46.6 | 0.000144 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 2 | AY.9 | 0.000135 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | AY.9.2.1 | 0.003953 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | B.1.1.216 | 0.001781 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | B.1.1.39 | 0.001019 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | B.1.177.81 | 0.000379 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 2 | B.1.232 | 0.000537 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 2 | B.1.232 | 0.000537 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 2 | 2 | B.1.258.17 | 0.000208 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 2 | 2 | B.6 | 0.00182 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | AY.59 | 0.00053 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B | 0.000128 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.1.158 | 0.012195 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.1.269 | 0.001353 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | B.1.1.302 | 0.002075 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.221.1 | 0.002907 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.320 | 0.001245 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 1 | B.1.329 | 0.000608 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctG | 1 | 1 | B.1.398 | 0.002976 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | B.1.474 | 0.001901 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | B.1.565 | 0.00081 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctA | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp1 | 4 | L4L | ctT | ctC | 1 | 1 | B.1.580 | 0.004065 |
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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