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/nsp6 | 139 | V139V | V3708V | syn | gtG | gtT | 1479 | 956 | 0.646383 | 11387-11389 |
ORF1ab/nsp6 | 139 | V139V | V3708V | syn | gtG | gtA | 1479 | 521 | 0.352265 | 11387-11389 |
ORF1ab/nsp6 | 139 | V139V | V3708V | syn | gtG | gtC | 1479 | 2 | 0.00135227 | 11387-11389 |
Details of the mutation V139V 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/nsp6 | 139 | V139V | gtG | gtT | 956 | 1479 | All | 0.000183 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 521 | 1479 | All | 0.0001 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtC | 2 | 1479 | All | 0 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 752 | 752 | AY.59 | 0.398305 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 216 | 220 | AY.44 | 0.001315 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 4 | 220 | AY.44 | 0.000024 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 137 | 144 | AY.4 | 0.000213 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 7 | 144 | AY.4 | 0.000011 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 37 | 73 | B.1.1.7 | 0.000033 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 36 | 73 | B.1.1.7 | 0.000032 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 49 | 49 | B.1.243.2 | 0.710145 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 26 | 33 | B.1.617.2 | 0.000098 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 7 | 33 | B.1.617.2 | 0.000026 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 21 | 21 | B.1.526 | 0.000494 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 14 | 14 | B.1.1.98 | 0.259259 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 8 | 13 | B.1.2 | 0.00007 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 3 | 13 | B.1.2 | 0.000026 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtC | 2 | 13 | B.1.2 | 0.000018 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 10 | 11 | AY.103 | 0.000062 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 11 | AY.103 | 0.000006 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 11 | 11 | AY.4.5 | 0.001182 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 5 | 9 | AY.25 | 0.00003 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 4 | 9 | AY.25 | 0.000024 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 9 | 9 | B.1.1 | 0.000163 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 7 | 8 | B.1 | 0.000064 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 8 | B.1 | 0.000009 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 7 | 8 | B.1.243 | 0.000487 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 8 | B.1.243 | 0.00007 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 4 | 7 | AY.75 | 0.000224 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 3 | 7 | AY.75 | 0.000168 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 6 | 6 | AY.27 | 0.000388 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 3 | 6 | AY.43 | 0.000013 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 3 | 6 | AY.43 | 0.000013 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 5 | 5 | AY.106 | 0.001674 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 4 | 4 | AY.76 | 0.019324 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 2 | 3 | AY.39.1 | 0.000079 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 3 | AY.39.1 | 0.00004 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 2 | 3 | B.1.258 | 0.000133 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 3 | B.1.258 | 0.000067 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 3 | 3 | B.1.627 | 0.006061 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 3 | 3 | P.1 | 0.000047 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 3 | 3 | P.1.17 | 0.000485 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 2 | 2 | AY.100 | 0.000092 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 2 | 2 | AY.102 | 0.000053 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 2 | AY.34 | 0.000097 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 2 | AY.34 | 0.000097 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 2 | AY.39 | 0.000025 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 2 | AY.39 | 0.000025 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 2 | 2 | AY.9.1 | 0.000167 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 2 | 2 | AY.98 | 0.000158 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 2 | 2 | B.1.279 | 0.001027 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 2 | 2 | B.1.36.8 | 0.002 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 2 | 2 | B.1.466.2 | 0.000782 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 2 | 2 | B.1.541 | 0.00885 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 2 | D.2 | 0.000075 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 2 | D.2 | 0.000075 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.105 | 0.000643 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.107 | 0.000466 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | AY.29.1 | 0.000221 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.1.290 | 0.018182 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.108 | 0.005814 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.177.12 | 0.000152 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.333 | 0.010526 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.36.17 | 0.000494 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.36.31 | 0.001751 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.446 | 0.02 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.590 | 0.004545 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | B.1.628 | 0.000352 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtT | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp6 | 139 | V139V | gtG | gtA | 1 | 1 | P.1.12 | 0.000484 |
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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