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 |
ORF6 | 30 | D30del2 | del | GAt | --t | 657 | 616 | 0.937595 | 27289-27291 | |
ORF6 | 30 | D30del2 | del | gAT | g-- | 657 | 40 | 0.0608828 | 27289-27291 | |
ORF6 | 30 | D30del2 | del | GAT | A-- | 657 | 1 | 0.00152207 | 27289-27291 |
Details of the mutation D30del2 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 |
ORF6 | 30 | D30del2 | GAt | --t | 616 | 657 | All | 0.000118 |
ORF6 | 30 | D30del2 | gAT | g-- | 40 | 657 | All | 0.000008 |
ORF6 | 30 | D30del2 | GAT | A-- | 1 | 657 | All | 0 |
ORF6 | 30 | D30del2 | GAt | --t | 198 | 206 | AY.4 | 0.000308 |
ORF6 | 30 | D30del2 | gAT | g-- | 8 | 206 | AY.4 | 0.000012 |
ORF6 | 30 | D30del2 | GAt | --t | 43 | 46 | B.1.1.7 | 0.000038 |
ORF6 | 30 | D30del2 | gAT | g-- | 3 | 46 | B.1.1.7 | 0.000003 |
ORF6 | 30 | D30del2 | GAt | --t | 35 | 44 | B.1.617.2 | 0.000132 |
ORF6 | 30 | D30del2 | gAT | g-- | 9 | 44 | B.1.617.2 | 0.000034 |
ORF6 | 30 | D30del2 | GAt | --t | 43 | 43 | AY.25 | 0.000259 |
ORF6 | 30 | D30del2 | GAt | --t | 23 | 24 | B.1.2 | 0.000203 |
ORF6 | 30 | D30del2 | gAT | g-- | 1 | 24 | B.1.2 | 0.000009 |
ORF6 | 30 | D30del2 | GAt | --t | 23 | 23 | B.1 | 0.000211 |
ORF6 | 30 | D30del2 | GAt | --t | 22 | 22 | AY.3 | 0.000219 |
ORF6 | 30 | D30del2 | GAt | --t | 20 | 20 | AY.44 | 0.000122 |
ORF6 | 30 | D30del2 | GAt | --t | 15 | 15 | AY.26 | 0.000425 |
ORF6 | 30 | D30del2 | gAT | g-- | 9 | 14 | AY.103 | 0.000056 |
ORF6 | 30 | D30del2 | GAt | --t | 5 | 14 | AY.103 | 0.000031 |
ORF6 | 30 | D30del2 | GAt | --t | 13 | 13 | B.1.526 | 0.000306 |
ORF6 | 30 | D30del2 | GAt | --t | 11 | 12 | AY.113 | 0.001566 |
ORF6 | 30 | D30del2 | gAT | g-- | 1 | 12 | AY.113 | 0.000142 |
ORF6 | 30 | D30del2 | GAt | --t | 10 | 11 | AY.43 | 0.000044 |
ORF6 | 30 | D30del2 | gAT | g-- | 1 | 11 | AY.43 | 0.000004 |
ORF6 | 30 | D30del2 | GAt | --t | 10 | 10 | AY.75 | 0.00056 |
ORF6 | 30 | D30del2 | GAt | --t | 6 | 8 | AY.20 | 0.000233 |
ORF6 | 30 | D30del2 | gAT | g-- | 2 | 8 | AY.20 | 0.000078 |
ORF6 | 30 | D30del2 | GAt | --t | 8 | 8 | AY.47 | 0.000249 |
ORF6 | 30 | D30del2 | GAt | --t | 7 | 7 | AY.54 | 0.000667 |
ORF6 | 30 | D30del2 | GAt | --t | 7 | 7 | B.1.351.2 | 0.002118 |
ORF6 | 30 | D30del2 | GAt | --t | 5 | 5 | AY.34 | 0.000485 |
ORF6 | 30 | D30del2 | GAt | --t | 5 | 5 | AY.4.2 | 0.000108 |
ORF6 | 30 | D30del2 | GAt | --t | 5 | 5 | AY.5 | 0.000103 |
ORF6 | 30 | D30del2 | GAt | --t | 5 | 5 | AY.9.2 | 0.000184 |
ORF6 | 30 | D30del2 | GAt | --t | 5 | 5 | B.1.177 | 0.000066 |
ORF6 | 30 | D30del2 | GAt | --t | 4 | 4 | AY.100 | 0.000184 |
ORF6 | 30 | D30del2 | GAt | --t | 4 | 4 | B.1.1.214 | 0.000222 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | AY.10 | 0.00159 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | AY.110 | 0.000338 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | AY.29 | 0.000047 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | AY.3.1 | 0.000256 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | AY.39 | 0.000074 |
ORF6 | 30 | D30del2 | gAT | g-- | 2 | 3 | AY.39.1 | 0.000079 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 3 | AY.39.1 | 0.00004 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | AY.42 | 0.000121 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | B.1.1 | 0.000054 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 3 | B.1.429 | 0.000047 |
ORF6 | 30 | D30del2 | gAT | g-- | 1 | 3 | B.1.429 | 0.000024 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 3 | B.1.596 | 0.000174 |
ORF6 | 30 | D30del2 | gAT | g-- | 1 | 3 | B.1.596 | 0.000087 |
ORF6 | 30 | D30del2 | GAt | --t | 3 | 3 | P.1 | 0.000047 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | AY.1 | 0.000791 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | AY.102 | 0.000053 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | AY.120 | 0.000074 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | AY.14 | 0.000176 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | AY.4.5 | 0.000215 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | AY.68 | 0.000547 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | B.1.177.18 | 0.00232 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 2 | B.1.177.21 | 0.000076 |
ORF6 | 30 | D30del2 | GAT | A-- | 1 | 2 | B.1.177.21 | 0.000076 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 2 | B.1.258 | 0.000067 |
ORF6 | 30 | D30del2 | gAT | g-- | 1 | 2 | B.1.258 | 0.000067 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | B.1.332 | 0.006993 |
ORF6 | 30 | D30del2 | GAt | --t | 2 | 2 | B.1.351 | 0.000059 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | A | 0.000387 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.106 | 0.000335 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.108 | 0.001103 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.119 | 0.000035 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.120.2 | 0.001285 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.30 | 0.000396 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.33 | 0.000067 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.36 | 0.000148 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.45 | 0.000122 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.46.5 | 0.000198 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.46.6 | 0.000072 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.59 | 0.00053 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.62 | 0.000436 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.75.1 | 0.00018 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.88 | 0.000884 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.9 | 0.000068 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.98 | 0.000079 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | AY.99.2 | 0.000092 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.1.222 | 0.000204 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.1.306 | 0.000438 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.1.33 | 0.000421 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.1.519 | 0.00004 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.1.83 | 0.00271 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.160 | 0.000031 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.177.5 | 0.001242 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.177.58 | 0.001332 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.258.17 | 0.000104 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.36.29 | 0.000517 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.36.38 | 0.001642 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.429.1 | 0.012048 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | B.1.595 | 0.000261 |
ORF6 | 30 | D30del2 | gAT | g-- | 1 | 1 | B.1.621 | 0.000089 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | P.1.14 | 0.000048 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | Q.1 | 0.000126 |
ORF6 | 30 | D30del2 | GAt | --t | 1 | 1 | R.1 | 0.00009 |
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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