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/nsp12 | 434 | S434F | S4826F | nonsyn | tCt | tTt | 1305 | 1304 | 0.999234 | 14740-14742 |
ORF1ab/nsp12 | 434 | S434F | S4826F | nonsyn | tCT | tTC | 1305 | 1 | 0.000766284 | 14740-14742 |
Details of the mutation S434F 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/nsp12 | 434 | S434F | tCt | tTt | 1304 | 1305 | All | 0.000249 |
ORF1ab/nsp12 | 434 | S434F | tCT | tTC | 1 | 1305 | All | 0 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 399 | 399 | B.1.1.7 | 0.000357 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 340 | 340 | B.1.142 | 0.985507 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 74 | 74 | B.1.177 | 0.000974 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 51 | 51 | B.1.617.2 | 0.000192 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 45 | 45 | AY.4 | 0.00007 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 37 | 37 | AZ.2 | 0.030378 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 33 | 33 | AY.9 | 0.002231 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 30 | 30 | AZ.1 | 0.026019 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 29 | 29 | B.1.2 | 0.000255 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 20 | 20 | B.1 | 0.000183 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 20 | 20 | B.1.1.277 | 0.015175 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 20 | 20 | B.1.621 | 0.00177 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 18 | 18 | B.1.628 | 0.006342 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 16 | 16 | AY.25 | 0.000096 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 14 | 14 | AY.102 | 0.000371 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 11 | 11 | B.1.429 | 0.000259 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 9 | 9 | AY.44 | 0.000055 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 9 | 9 | B.1.1 | 0.000163 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 9 | 9 | B.1.526 | 0.000212 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 7 | 7 | AY.43 | 0.000031 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 6 | 6 | AY.39 | 0.000148 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 5 | 5 | AY.3 | 0.00005 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 5 | 5 | AY.45 | 0.000608 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 5 | 5 | C.16 | 0.005302 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 4 | 4 | AY.5 | 0.000083 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 4 | 4 | B.1.459 | 0.016327 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 3 | 3 | AY.118 | 0.000188 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 3 | 3 | B.1.1.222 | 0.000612 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 3 | 3 | P.1 | 0.000047 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | AY.103 | 0.000012 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | AY.33 | 0.000134 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | AY.34 | 0.000194 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | AY.39.1 | 0.000079 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | AY.42 | 0.00008 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | AY.63 | 0.000774 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | AY.67 | 0.000929 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | B.1.1.464 | 0.002946 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | B.1.177.4 | 0.000422 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | B.1.177.73 | 0.001133 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | B.1.243 | 0.000139 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | B.1.427 | 0.000101 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 2 | 2 | B.1.596 | 0.000174 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | 0.055556 | |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.46 | 0.000104 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.58 | 0.000907 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.64 | 0.000595 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.82 | 0.001357 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.113 | 0.006993 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.189 | 0.001513 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.279 | 0.001121 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.286 | 0.002899 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.22 | 0.001318 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.351.2 | 0.000303 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp12 | 434 | S434F | tCT | tTC | 1 | 1 | B.1.377 | 0.004566 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.383 | 0.009009 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.400 | 0.000429 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.557 | 0.05 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.588 | 0.00091 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | K.1 | 0.02381 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | N.9 | 0.005952 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | P.1.14 | 0.000048 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp12 | 434 | S434F | tCt | tTt | 1 | 1 | Q.8 | 0.000165 |
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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