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 | 862 | L862F | L1680F | nonsyn | ttG | ttT | 1101 | 888 | 0.80654 | 5303-5305 |
ORF1ab/nsp3 | 862 | L862F | L1680F | nonsyn | ttG | ttC | 1101 | 213 | 0.19346 | 5303-5305 |
Details of the mutation L862F 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 | 862 | L862F | ttG | ttT | 888 | 1101 | All | 0.00017 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 213 | 1101 | All | 0.000041 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 123 | 209 | AY.4 | 0.000191 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 86 | 209 | AY.4 | 0.000134 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 162 | 173 | B.1.617.2 | 0.00061 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 11 | 173 | B.1.617.2 | 0.000041 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 79 | 85 | B.1.1.7 | 0.000071 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 6 | 85 | B.1.1.7 | 0.000005 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 76 | 76 | AY.43 | 0.000337 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 37 | 44 | B.1.2 | 0.000326 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 7 | 44 | B.1.2 | 0.000062 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 30 | 44 | D.2 | 0.002251 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 14 | 44 | D.2 | 0.001051 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 40 | 40 | AY.3 | 0.000398 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 38 | 39 | B.1 | 0.000348 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 39 | B.1 | 0.000009 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 34 | 35 | AY.33 | 0.00227 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 35 | AY.33 | 0.000067 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 35 | 35 | AY.44 | 0.000213 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 24 | 24 | AY.120 | 0.000892 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 21 | 21 | AY.25 | 0.000126 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 17 | 17 | AY.102 | 0.000451 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 17 | 17 | B.1.429 | 0.0004 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 15 | 16 | B.1.1 | 0.000272 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 16 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 16 | 16 | P.2 | 0.002986 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 12 | 13 | AY.103 | 0.000075 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 13 | AY.103 | 0.000006 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 11 | 11 | AY.7.1 | 0.00124 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 9 | 10 | AY.39 | 0.000222 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 10 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 10 | 10 | AY.71 | 0.004751 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 10 | 10 | B.1.1.28 | 0.003112 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 8 | 8 | AY.26 | 0.000226 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 8 | 8 | B.1.36.1 | 0.009122 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 7 | 7 | B.1.561 | 0.002779 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 5 | 5 | AY.56 | 0.008026 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 5 | 5 | AY.81 | 0.00996 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 5 | 5 | B.1.240.2 | 0.151515 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 4 | 5 | B.1.258 | 0.000266 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 5 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 4 | AY.119 | 0.000106 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 4 | AY.119 | 0.000035 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 4 | 4 | AY.9 | 0.00027 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 4 | 4 | B.1.177 | 0.000053 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 4 | 4 | P.1 | 0.000063 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 3 | AY.100 | 0.000138 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 3 | AY.20 | 0.000117 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 3 | AY.47 | 0.000093 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 3 | AY.5 | 0.000062 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 3 | B.1.160 | 0.000094 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 3 | B.1.177.81 | 0.000568 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 3 | B.1.223 | 0.005556 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 3 | B.1.223 | 0.002778 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 3 | 3 | Q.4 | 0.001364 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | AY.76 | 0.009662 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | AY.9.2 | 0.000073 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | AY.98.1 | 0.000097 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.1.326 | 0.003521 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.1.420 | 0.002012 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.177.54 | 0.001213 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.241 | 0.001623 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.258.17 | 0.000208 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.367 | 0.001585 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.507 | 0.022472 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | B.1.525 | 0.000226 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | P.1.17 | 0.000324 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 2 | 2 | P.1.4 | 0.001953 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | A.2.2 | 0.001689 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 1 | AY.101 | 0.00049 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.11 | 0.001339 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.113 | 0.000142 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.16.1 | 0.00047 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 1 | AY.40 | 0.000964 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.59 | 0.00053 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.68 | 0.000274 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.82 | 0.001357 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.90 | 0.000684 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 1 | B.1.1.10 | 0.001115 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.1.216 | 0.00089 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.1.284 | 0.000107 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttC | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.1.74 | 0.00431 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.104 | 0.00369 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.177.77 | 0.000726 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.36.16 | 0.001425 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.36.22 | 0.001208 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.36.29 | 0.000517 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.398 | 0.002976 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.422 | 0.000812 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.582 | 0.000491 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp3 | 862 | L862F | ttG | ttT | 1 | 1 | W.4 | 0.001351 |
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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