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 | 300 | P300S | P5624S | nonsyn | Cct | Tct | 871 | 866 | 0.994259 | 17134-17136 |
ORF1ab/nsp13 | 300 | P300S | P5624S | nonsyn | CcT | TcA | 871 | 3 | 0.00344432 | 17134-17136 |
ORF1ab/nsp13 | 300 | P300S | P5624S | nonsyn | CcT | TcG | 871 | 2 | 0.00229621 | 17134-17136 |
Details of the mutation P300S 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 | 300 | P300S | Cct | Tct | 866 | 871 | All | 0.000166 |
ORF1ab/nsp13 | 300 | P300S | CcT | TcA | 3 | 871 | All | 0.000001 |
ORF1ab/nsp13 | 300 | P300S | CcT | TcG | 2 | 871 | All | 0 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 468 | 473 | B.1.1.7 | 0.000419 |
ORF1ab/nsp13 | 300 | P300S | CcT | TcA | 3 | 473 | B.1.1.7 | 0.000003 |
ORF1ab/nsp13 | 300 | P300S | CcT | TcG | 2 | 473 | B.1.1.7 | 0.000002 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 48 | 48 | B.1.604 | 0.827586 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 40 | 40 | AY.4 | 0.000062 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 27 | 27 | B.1.617.1 | 0.003482 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 26 | 26 | AY.25 | 0.000156 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 24 | 24 | B.1.177 | 0.000316 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 15 | 15 | B.1.1 | 0.000272 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 13 | 13 | B.1 | 0.000119 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 11 | 11 | AY.119 | 0.000388 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 10 | 10 | AY.43 | 0.000044 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 9 | 9 | B.1.2 | 0.000079 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 9 | 9 | B.1.258 | 0.000599 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 8 | 8 | P.1 | 0.000126 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 7 | 7 | B.1.617.2 | 0.000026 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 6 | 6 | B.1.177.12 | 0.00091 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 6 | 6 | B.1.351 | 0.000178 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 6 | 6 | B.1.621.1 | 0.003035 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 5 | 5 | AY.3 | 0.00005 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 5 | 5 | AY.44 | 0.00003 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 5 | 5 | B.1.525 | 0.000566 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 4 | 4 | AY.39 | 0.000099 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 4 | 4 | B.1.1.28 | 0.001245 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 4 | 4 | B.1.160 | 0.000125 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 4 | 4 | B.1.9.4 | 0.02454 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 4 | 4 | C.37 | 0.000464 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | AY.38 | 0.001498 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | AY.6 | 0.000123 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | AY.60 | 0.002814 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | AY.98 | 0.000237 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | AY.98.1 | 0.000145 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | B.1.177.77 | 0.002179 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | B.1.36.29 | 0.001552 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | B.1.429 | 0.000071 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | B.1.526 | 0.000071 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 3 | 3 | D.2 | 0.000225 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | A | 0.000774 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | AU.2 | 0.004843 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | AY.111 | 0.000366 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | AY.29.1 | 0.000441 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | AY.34 | 0.000194 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | AY.47 | 0.000062 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | AY.5 | 0.000041 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | B.1.243 | 0.000139 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | B.1.258.17 | 0.000208 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | B.1.258.21 | 0.015504 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | A.21 | 0.00277 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.103 | 0.000006 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.12 | 0.000316 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.2 | 0.000356 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.35 | 0.000233 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.70 | 0.000209 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.71 | 0.000475 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.76 | 0.004831 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.1.157 | 0.000913 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.1.277 | 0.000759 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.1.284 | 0.000107 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.1.354 | 0.004386 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.1.485 | 0.016667 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.134 | 0.005464 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.177.52 | 0.001757 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.232 | 0.000537 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.36.21 | 0.00216 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.400 | 0.000429 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.428 | 0.00102 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.546 | 0.003704 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | C.16 | 0.00106 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 1 | 1 | P.1.7 | 0.000319 |
ORF1ab/nsp13 | 300 | P300S | Cct | Tct | 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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