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 | 533 | V533V | V5857V | syn | gtT | gtC | 535 | 472 | 0.882243 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533V | V5857V | syn | gtT | gtA | 535 | 53 | 0.0990654 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533V | V5857V | syn | gtT | gtG | 535 | 10 | 0.0186916 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533G | V5857G | nonsyn | gTt | gGt | 24 | 24 | 1 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533del | V5857del | del | GTT | --- | 17 | 17 | 1 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533A | V5857A | nonsyn | gTt | gCt | 10 | 10 | 1 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533F | V5857F | nonsyn | Gtt | Ttt | 7 | 7 | 1 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533del1 | V5857del1 | del | Gtt | -tt | 5 | 3 | 0.6 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533del1 | V5857del1 | del | gTt | g-t | 5 | 2 | 0.4 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533L | V5857L | nonsyn | Gtt | Ctt | 4 | 4 | 1 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533I | V5857I | nonsyn | Gtt | Att | 4 | 4 | 1 | 17833-17835 |
ORF1ab/nsp13 | 533 | V533D | V5857D | nonsyn | gTt | gAt | 2 | 2 | 1 | 17833-17835 |
Details of the mutation no 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 | 533 | V533V | gtT | gtC | 472 | 535 | All | 0.00009 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 53 | 535 | All | 0.00001 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtG | 10 | 535 | All | 0.000002 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 127 | 132 | B.1.1.7 | 0.000114 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 4 | 132 | B.1.1.7 | 0.000004 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtG | 1 | 132 | B.1.1.7 | 0.000001 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 93 | 93 | B.1.2 | 0.000819 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 88 | 88 | B.1.76 | 1 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 35 | 35 | AY.44 | 0.000213 |
ORF1ab/nsp13 | 533 | V533G | gTt | gGt | 24 | 24 | All | 0.000005 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 17 | 18 | B.1.617.2 | 0.000064 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 18 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 17 | 17 | All | 0.000003 |
ORF1ab/nsp13 | 533 | V533G | gTt | gGt | 17 | 17 | AY.4 | 0.000026 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 11 | 16 | B.1.1 | 0.0002 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 5 | 16 | B.1.1 | 0.000091 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 11 | 15 | AY.4 | 0.000017 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtG | 4 | 15 | AY.4 | 0.000006 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 15 | 15 | B.1.243 | 0.001044 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 14 | 14 | B.1.609 | 0.006711 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 10 | 10 | All | 0.000002 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 8 | 8 | AY.103 | 0.00005 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 7 | 8 | AY.43 | 0.000031 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 8 | AY.43 | 0.000004 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 8 | 8 | B.1 | 0.000073 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 7 | 7 | All | 0.000001 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 7 | 7 | AY.119 | 0.000247 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 7 | 7 | P.1.15 | 0.001626 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 6 | 6 | B.1.258 | 0.000399 |
ORF1ab/nsp13 | 533 | V533del1 | Gtt | -tt | 3 | 5 | All | 0.000001 |
ORF1ab/nsp13 | 533 | V533del1 | gTt | g-t | 2 | 5 | All | 0 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 3 | 5 | B.1.177 | 0.00004 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 2 | 5 | B.1.177 | 0.000026 |
ORF1ab/nsp13 | 533 | V533L | Gtt | Ctt | 4 | 4 | All | 0.000001 |
ORF1ab/nsp13 | 533 | V533I | Gtt | Att | 4 | 4 | All | 0.000001 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 4 | 4 | B.1.351 | 0.000119 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 3 | 4 | B.1.637 | 0.000219 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 4 | B.1.637 | 0.000073 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 3 | 3 | AY.19 | 0.003421 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 2 | 3 | AY.26 | 0.000057 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtG | 1 | 3 | AY.26 | 0.000028 |
ORF1ab/nsp13 | 533 | V533del1 | gTt | g-t | 2 | 3 | B.1 | 0.000018 |
ORF1ab/nsp13 | 533 | V533del1 | Gtt | -tt | 1 | 3 | B.1 | 0.000009 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 3 | 3 | B.1.1.214 | 0.000166 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 3 | 3 | B.1.1.28 | 0.000934 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 3 | 3 | B.1.1.7 | 0.000003 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtG | 2 | 3 | D.2 | 0.00015 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 3 | D.2 | 0.000075 |
ORF1ab/nsp13 | 533 | V533D | gTt | gAt | 2 | 2 | All | 0 |
ORF1ab/nsp13 | 533 | V533G | gTt | gGt | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp13 | 533 | V533G | gTt | gGt | 2 | 2 | AY.43 | 0.000009 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 2 | 2 | AY.46 | 0.000208 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 2 | 2 | AY.46.2 | 0.001271 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 2 | 2 | AY.81 | 0.003984 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 2 | 2 | B.1.1.7 | 0.000002 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 2 | 2 | B.1.177.73 | 0.001133 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 2 | 2 | B.1.621 | 0.000177 |
ORF1ab/nsp13 | 533 | V533L | Gtt | Ctt | 1 | 1 | 0.055556 | |
ORF1ab/nsp13 | 533 | V533I | Gtt | Att | 1 | 1 | AU.1 | 0.001266 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | AY.116.1 | 0.000311 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtG | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp13 | 533 | V533G | gTt | gGt | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF1ab/nsp13 | 533 | V533L | Gtt | Ctt | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp13 | 533 | V533I | Gtt | Att | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp13 | 533 | V533G | gTt | gGt | 1 | 1 | AY.46.5 | 0.000198 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp13 | 533 | V533G | gTt | gGt | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | B.1.1.446 | 0.076923 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | B.1.1.63 | 0.000386 |
ORF1ab/nsp13 | 533 | V533L | Gtt | Ctt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp13 | 533 | V533I | Gtt | Att | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | B.1.177.86 | 0.000183 |
ORF1ab/nsp13 | 533 | V533D | gTt | gAt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.214 | 0.003663 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtG | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp13 | 533 | V533D | gTt | gAt | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.258.7 | 0.001912 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 1 | 1 | B.1.320 | 0.001245 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.324 | 0.001605 |
ORF1ab/nsp13 | 533 | V533F | Gtt | Ttt | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.396 | 0.000706 |
ORF1ab/nsp13 | 533 | V533del1 | Gtt | -tt | 1 | 1 | B.1.533 | 0.009615 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 533 | V533L | Gtt | Ctt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp13 | 533 | V533A | gTt | gCt | 1 | 1 | B.6.5 | 0.076923 |
ORF1ab/nsp13 | 533 | V533del | GTT | --- | 1 | 1 | C.17 | 0.055556 |
ORF1ab/nsp13 | 533 | V533I | Gtt | Att | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtA | 1 | 1 | P.1.7 | 0.000319 |
ORF1ab/nsp13 | 533 | V533V | gtT | gtC | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp13 | 533 | V533del1 | Gtt | -tt | 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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