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 |
S | 407 | V407V | syn | gtC | gtT | 4568 | 4486 | 0.982049 | 22781-22783 | |
S | 407 | V407V | syn | gtC | gtA | 4568 | 81 | 0.017732 | 22781-22783 | |
S | 407 | V407V | syn | gtC | gtG | 4568 | 1 | 0.000218914 | 22781-22783 |
Details of the mutation V407V 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 |
S | 407 | V407V | gtC | gtT | 4486 | 4568 | All | 0.000858 |
S | 407 | V407V | gtC | gtA | 81 | 4568 | All | 0.000015 |
S | 407 | V407V | gtC | gtG | 1 | 4568 | All | 0 |
S | 407 | V407V | gtC | gtT | 2376 | 2376 | AY.3 | 0.023633 |
S | 407 | V407V | gtC | gtT | 786 | 793 | AY.25 | 0.004728 |
S | 407 | V407V | gtC | gtA | 7 | 793 | AY.25 | 0.000042 |
S | 407 | V407V | gtC | gtT | 582 | 582 | AY.82 | 0.789688 |
S | 407 | V407V | gtC | gtT | 188 | 188 | B.1.1 | 0.00341 |
S | 407 | V407V | gtC | gtT | 99 | 99 | B.1.1.251 | 0.785714 |
S | 407 | V407V | gtC | gtT | 71 | 84 | B.1.1.7 | 0.000064 |
S | 407 | V407V | gtC | gtA | 13 | 84 | B.1.1.7 | 0.000012 |
S | 407 | V407V | gtC | gtT | 66 | 69 | B.1.617.2 | 0.000249 |
S | 407 | V407V | gtC | gtA | 3 | 69 | B.1.617.2 | 0.000011 |
S | 407 | V407V | gtC | gtT | 23 | 28 | B.1 | 0.000211 |
S | 407 | V407V | gtC | gtA | 5 | 28 | B.1 | 0.000046 |
S | 407 | V407V | gtC | gtA | 27 | 27 | AY.4.2 | 0.000586 |
S | 407 | V407V | gtC | gtT | 23 | 23 | AY.1 | 0.009102 |
S | 407 | V407V | gtC | gtT | 20 | 22 | AY.43 | 0.000089 |
S | 407 | V407V | gtC | gtA | 2 | 22 | AY.43 | 0.000009 |
S | 407 | V407V | gtC | gtT | 19 | 19 | AY.117 | 0.001606 |
S | 407 | V407V | gtC | gtT | 18 | 18 | AY.119 | 0.000636 |
S | 407 | V407V | gtC | gtT | 17 | 17 | AY.4 | 0.000026 |
S | 407 | V407V | gtC | gtT | 17 | 17 | AY.44 | 0.000103 |
S | 407 | V407V | gtC | gtT | 10 | 12 | AY.103 | 0.000062 |
S | 407 | V407V | gtC | gtA | 2 | 12 | AY.103 | 0.000012 |
S | 407 | V407V | gtC | gtT | 12 | 12 | B.1.575.1 | 0.029268 |
S | 407 | V407V | gtC | gtT | 10 | 11 | B.1.351 | 0.000297 |
S | 407 | V407V | gtC | gtA | 1 | 11 | B.1.351 | 0.00003 |
S | 407 | V407V | gtC | gtT | 11 | 11 | P.1.16 | 0.004115 |
S | 407 | V407V | gtC | gtT | 7 | 10 | P.1 | 0.00011 |
S | 407 | V407V | gtC | gtA | 3 | 10 | P.1 | 0.000047 |
S | 407 | V407V | gtC | gtT | 8 | 8 | C.37 | 0.000929 |
S | 407 | V407V | gtC | gtT | 7 | 7 | AY.55 | 0.006422 |
S | 407 | V407V | gtC | gtT | 6 | 6 | B.1.2 | 0.000053 |
S | 407 | V407V | gtC | gtT | 6 | 6 | B.1.232 | 0.003224 |
S | 407 | V407V | gtC | gtA | 5 | 5 | AY.20 | 0.000194 |
S | 407 | V407V | gtC | gtT | 5 | 5 | AY.5 | 0.000103 |
S | 407 | V407V | gtC | gtT | 5 | 5 | AY.75 | 0.00028 |
S | 407 | V407V | gtC | gtT | 4 | 5 | B.1.177 | 0.000053 |
S | 407 | V407V | gtC | gtA | 1 | 5 | B.1.177 | 0.000013 |
S | 407 | V407V | gtC | gtT | 4 | 4 | AY.102 | 0.000106 |
S | 407 | V407V | gtC | gtT | 3 | 4 | AY.26 | 0.000085 |
S | 407 | V407V | gtC | gtA | 1 | 4 | AY.26 | 0.000028 |
S | 407 | V407V | gtC | gtT | 4 | 4 | AY.9.2 | 0.000147 |
S | 407 | V407V | gtC | gtT | 3 | 4 | B.1.526 | 0.000071 |
S | 407 | V407V | gtC | gtA | 1 | 4 | B.1.526 | 0.000024 |
S | 407 | V407V | gtC | gtT | 4 | 4 | P.1.15 | 0.000929 |
S | 407 | V407V | gtC | gtT | 3 | 3 | AY.46.1 | 0.00308 |
S | 407 | V407V | gtC | gtT | 3 | 3 | AY.79 | 0.003632 |
S | 407 | V407V | gtC | gtT | 3 | 3 | B.1.311 | 0.000824 |
S | 407 | V407V | gtC | gtT | 3 | 3 | B.1.36.18 | 0.001261 |
S | 407 | V407V | gtC | gtT | 2 | 3 | B.1.427 | 0.000101 |
S | 407 | V407V | gtC | gtA | 1 | 3 | B.1.427 | 0.00005 |
S | 407 | V407V | gtC | gtT | 3 | 3 | C.37.1 | 0.007853 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.121 | 0.000271 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.13 | 0.000322 |
S | 407 | V407V | gtC | gtT | 1 | 2 | AY.16.1 | 0.00047 |
S | 407 | V407V | gtC | gtA | 1 | 2 | AY.16.1 | 0.00047 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.29 | 0.000032 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.4.5 | 0.000215 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.42 | 0.00008 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.45 | 0.000243 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.62 | 0.000871 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.84 | 0.000875 |
S | 407 | V407V | gtC | gtT | 2 | 2 | AY.9 | 0.000135 |
S | 407 | V407V | gtC | gtT | 2 | 2 | B.1.1.234 | 0.024096 |
S | 407 | V407V | gtC | gtT | 2 | 2 | B.1.369 | 0.00057 |
S | 407 | V407V | gtC | gtT | 2 | 2 | B.1.621 | 0.000177 |
S | 407 | V407V | gtC | gtT | 2 | 2 | D.2 | 0.00015 |
S | 407 | V407V | gtC | gtT | 1 | 1 | 0.055556 | |
S | 407 | V407V | gtC | gtA | 1 | 1 | A | 0.000387 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AD.2 | 0.000219 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.100 | 0.000046 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.113 | 0.000142 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.3.1 | 0.000085 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.39 | 0.000025 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.39.1 | 0.00004 |
S | 407 | V407V | gtC | gtA | 1 | 1 | AY.4.2.1 | 0.000149 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.46 | 0.000104 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.5.3 | 0.000337 |
S | 407 | V407V | gtC | gtA | 1 | 1 | AY.52 | 0.000814 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.56 | 0.001605 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.59 | 0.00053 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.9.1 | 0.000084 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.93 | 0.000273 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.95 | 0.000761 |
S | 407 | V407V | gtC | gtT | 1 | 1 | AY.98.1 | 0.000048 |
S | 407 | V407V | gtC | gtA | 1 | 1 | B | 0.000128 |
S | 407 | V407V | gtC | gtA | 1 | 1 | B.1.1.221 | 0.010101 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.177.17 | 0.000821 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.177.75 | 0.001041 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.177.8 | 0.000752 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.240 | 0.000216 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.429 | 0.000024 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.466.2 | 0.000391 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.595 | 0.000261 |
S | 407 | V407V | gtC | gtA | 1 | 1 | B.1.596 | 0.000087 |
S | 407 | V407V | gtC | gtA | 1 | 1 | B.1.623 | 0.000536 |
S | 407 | V407V | gtC | gtG | 1 | 1 | B.1.630 | 0.005236 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.631 | 0.003367 |
S | 407 | V407V | gtC | gtA | 1 | 1 | B.1.91 | 0.002075 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.1.94 | 0.027027 |
S | 407 | V407V | gtC | gtT | 1 | 1 | B.4.4 | 0.018868 |
S | 407 | V407V | gtC | gtT | 1 | 1 | P.1.2 | 0.001156 |
S | 407 | V407V | gtC | gtT | 1 | 1 | Q.8 | 0.000165 |
S | 407 | V407V | gtC | gtT | 1 | 1 | W.1 | 0.008696 |
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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