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/nsp1 | 60 | V60del | V60del | del | GTT | --- | 529 | 529 | 1 | 443-445 |
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/nsp1 | 60 | V60del | GTT | --- | 529 | 529 | All | 0.000101 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 138 | 138 | AY.4 | 0.000215 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 68 | 68 | B.1.1.7 | 0.000061 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 45 | 45 | B.1.617.2 | 0.000169 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 22 | 22 | AY.44 | 0.000134 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 16 | 16 | AY.25 | 0.000096 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 16 | 16 | AY.43 | 0.000071 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 13 | 13 | AY.26 | 0.000368 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 11 | 11 | AY.5 | 0.000227 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 9 | 9 | AY.4.2 | 0.000195 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 8 | 8 | AY.103 | 0.00005 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 8 | 8 | AY.3 | 0.00008 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 8 | 8 | AY.33 | 0.000534 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 7 | 7 | AY.29 | 0.00011 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 7 | 7 | AY.90 | 0.004791 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 6 | 6 | B.1.1.285 | 0.039216 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 5 | 5 | AT.1 | 0.025641 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 5 | 5 | AY.102 | 0.000133 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 5 | 5 | B.1 | 0.000046 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 4 | 4 | AY.119 | 0.000141 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 4 | 4 | AY.9.2 | 0.000147 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 4 | 4 | B.1.1.33 | 0.001684 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 4 | 4 | B.1.1.348 | 0.003185 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | AY.39 | 0.000074 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | AY.4.5 | 0.000322 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | AY.54 | 0.000286 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | AY.6 | 0.000123 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | AY.61 | 0.000314 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | AY.95 | 0.002283 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | AY.98.1 | 0.000145 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 3 | 3 | B.1.2 | 0.000026 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | 0.111111 | |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | AY.116 | 0.000574 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | AY.46.6 | 0.000144 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | B.1.128 | 0.001271 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | B.1.36.17 | 0.000988 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | N.4 | 0.008511 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | N.6 | 0.014184 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 2 | 2 | P.2 | 0.000373 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | A | 0.000387 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.1 | 0.000396 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.11 | 0.001339 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.19 | 0.00114 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.35 | 0.000233 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.46.5 | 0.000198 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.7 | 0.000196 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.71 | 0.000475 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.170 | 0.001247 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.232 | 0.001815 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.25 | 0.000569 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.298 | 0.000862 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.322 | 0.008772 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.108 | 0.005814 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.149 | 0.003425 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.11 | 0.001698 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.16 | 0.000664 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.18 | 0.00116 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.65 | 0.000665 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.177.9 | 0.001332 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.179 | 0.003759 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.280 | 0.007143 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.526 | 0.000024 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | B.23 | 0.002924 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | P.1.12 | 0.000484 |
ORF1ab/nsp1 | 60 | V60del | GTT | --- | 1 | 1 | P.1.9 | 0.004808 |
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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