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/nsp15A1-B | 257 | R257L | R6709L | nonsyn | cGt | cTt | 379 | 378 | 0.997361 | 20389-20391 |
ORF1ab/nsp15A1-B | 257 | R257L | R6709L | nonsyn | cGT | cTA | 379 | 1 | 0.00263852 | 20389-20391 |
Details of the mutation R257L 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/nsp15A1-B | 257 | R257L | cGt | cTt | 378 | 379 | All | 0.000072 |
ORF1ab/nsp15A1-B | 257 | R257L | cGT | cTA | 1 | 379 | All | 0 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 70 | 70 | AY.4 | 0.000109 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 47 | 47 | B.1.617.2 | 0.000177 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 23 | 23 | AY.103 | 0.000143 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 20 | 20 | AY.44 | 0.000122 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 16 | 16 | AY.43 | 0.000071 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 14 | 14 | AY.26 | 0.000396 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 12 | 12 | AY.25 | 0.000072 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 12 | 12 | B.1.1.7 | 0.000011 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 10 | 10 | AY.3 | 0.000099 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 9 | 9 | B.1.243 | 0.000626 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 8 | 8 | AY.42 | 0.000322 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 8 | 8 | B.1.429 | 0.000188 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 7 | 7 | AY.102 | 0.000186 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 7 | 7 | AY.36 | 0.001037 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 6 | 6 | AY.98.1 | 0.000291 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 6 | 6 | B.1.2 | 0.000053 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 6 | 6 | B.1.436 | 0.006173 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 5 | 5 | AY.4.5 | 0.000537 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 5 | 5 | B.1 | 0.000046 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 4 | 4 | AY.119 | 0.000141 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 4 | 4 | AY.19 | 0.004561 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 4 | 4 | B.1.1 | 0.000073 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | AY.23 | 0.000209 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | AY.29 | 0.000047 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | AY.33 | 0.0002 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | AY.39 | 0.000074 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | AY.47 | 0.000093 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | AY.5 | 0.000062 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | AY.9 | 0.000203 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 3 | 3 | B.1.111 | 0.003525 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | A.1 | 0.000564 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | AY.116 | 0.000574 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | AY.95 | 0.001522 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | AY.99.2 | 0.000184 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | B.1.1.304 | 0.005618 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 2 | 2 | B.1.36.17 | 0.000988 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | A.19 | 0.009434 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.118 | 0.000063 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.17 | 0.008197 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.39.1.1 | 0.000725 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.46.6 | 0.000072 |
ORF1ab/nsp15A1-B | 257 | R257L | cGT | cTA | 1 | 1 | AY.59 | 0.00053 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.80 | 0.001129 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.87 | 0.000833 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.1.10 | 0.001115 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.1.186 | 0.003436 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.1.216 | 0.00089 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.1.339 | 0.010526 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.1.39 | 0.00051 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.1.51 | 0.001718 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.206 | 0.000816 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp15A1-B | 257 | R257L | cGt | cTt | 1 | 1 | B.1.595 | 0.000261 |
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
|