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 |
S | 1116 | T1116T | syn | acT | acC | 26291 | 26244 | 0.998212 | 24908-24910 |
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 |
S | 1116 | T1116T | acT | acC | 26244 | 26291 | All | 0.005019 |
S | 1116 | T1116T | acT | acC | 10402 | 10402 | B.1.258 | 0.692221 |
S | 1116 | T1116T | acT | acC | 9594 | 9594 | B.1.258.17 | 0.997505 |
S | 1116 | T1116T | acT | acC | 2467 | 2467 | B.1.258.11 | 0.977804 |
S | 1116 | T1116T | acT | acC | 740 | 746 | B.1.1.7 | 0.000662 |
S | 1116 | T1116T | acT | acC | 522 | 522 | B.1.258.7 | 0.998088 |
S | 1116 | T1116T | acT | acC | 368 | 368 | B.1.258.22 | 0.981333 |
S | 1116 | T1116T | acT | acC | 322 | 322 | B.1 | 0.002949 |
S | 1116 | T1116T | acT | acC | 289 | 289 | B.1.258.4 | 0.996552 |
S | 1116 | T1116T | acT | acC | 200 | 200 | B.1.258.9 | 1 |
S | 1116 | T1116T | acT | acC | 141 | 141 | B.1.258.19 | 1 |
S | 1116 | T1116T | acT | acC | 127 | 127 | B.1.258.21 | 0.984496 |
S | 1116 | T1116T | acT | acC | 125 | 125 | B.1.258.12 | 0.984252 |
S | 1116 | T1116T | acT | acC | 114 | 114 | B.1.258.5 | 1 |
S | 1116 | T1116T | acT | acC | 87 | 87 | B.1.258.10 | 0.988636 |
S | 1116 | T1116T | acT | acC | 54 | 73 | B.1.177 | 0.000711 |
S | 1116 | T1116T | acT | acC | 63 | 63 | B.1.258.20 | 1 |
S | 1116 | T1116T | acT | acC | 51 | 51 | B.1.258.6 | 1 |
S | 1116 | T1116T | acT | acC | 50 | 50 | B.1.160 | 0.001559 |
S | 1116 | T1116T | acT | acC | 42 | 42 | B.1.258.23 | 1 |
S | 1116 | T1116T | acT | acC | 39 | 39 | B.1.1 | 0.000707 |
S | 1116 | T1116T | acT | acC | 35 | 35 | Q.1 | 0.004421 |
S | 1116 | T1116T | acT | acC | 32 | 32 | B.1.609 | 0.01534 |
S | 1116 | T1116T | acT | acC | 31 | 31 | B.1.258.24 | 0.333333 |
S | 1116 | T1116T | acT | acC | 27 | 28 | AY.75 | 0.001513 |
S | 1116 | T1116T | acT | acC | 25 | 25 | B.1.234 | 0.003299 |
S | 1116 | T1116T | acT | acC | 15 | 23 | AY.103 | 0.000093 |
S | 1116 | T1116T | acT | acC | 18 | 18 | B | 0.002301 |
S | 1116 | T1116T | acT | acC | 15 | 15 | AY.43 | 0.000066 |
S | 1116 | T1116T | acT | acC | 13 | 13 | B.1.1.222 | 0.002652 |
S | 1116 | T1116T | acT | acC | 13 | 13 | B.1.258.14 | 0.012745 |
S | 1116 | T1116T | acT | acC | 10 | 11 | B.1.221 | 0.00071 |
S | 1116 | T1116T | acT | acC | 9 | 10 | AY.4 | 0.000014 |
S | 1116 | T1116T | acT | acC | 6 | 10 | AY.44 | 0.000037 |
S | 1116 | T1116T | acT | acC | 10 | 10 | B.1.258.18 | 1 |
S | 1116 | T1116T | acT | acC | 8 | 8 | B.1.375 | 0.006557 |
S | 1116 | T1116T | acT | acC | 7 | 7 | A | 0.002709 |
S | 1116 | T1116T | acT | acC | 6 | 7 | B.1.2 | 0.000053 |
S | 1116 | T1116T | acT | acC | 7 | 7 | B.1.222 | 0.011844 |
S | 1116 | T1116T | acT | acC | 6 | 7 | B.1.617.2 | 0.000023 |
S | 1116 | T1116T | acT | acC | 7 | 7 | B.4.1 | 0.132075 |
S | 1116 | T1116T | acT | acC | 6 | 6 | B.1.177.86 | 0.001101 |
S | 1116 | T1116T | acT | acC | 5 | 5 | AY.25 | 0.00003 |
S | 1116 | T1116T | acT | acC | 5 | 5 | B.1.177.73 | 0.002831 |
S | 1116 | T1116T | acT | acC | 5 | 5 | B.1.411 | 0.018519 |
S | 1116 | T1116T | acT | acC | 5 | 5 | B.1.600 | 0.02924 |
S | 1116 | T1116T | acT | acC | 4 | 4 | B.1.1.216 | 0.003562 |
S | 1116 | T1116T | acT | acC | 4 | 4 | B.1.1.39 | 0.002039 |
S | 1116 | T1116T | acT | acC | 4 | 4 | B.1.126 | 0.005102 |
S | 1116 | T1116T | acT | acC | 4 | 4 | B.1.177.21 | 0.000306 |
S | 1116 | T1116T | acT | acC | 4 | 4 | B.1.177.6 | 0.003906 |
S | 1116 | T1116T | acT | acC | 2 | 3 | 0.111111 | |
S | 1116 | T1116T | acT | acC | 3 | 3 | AY.3 | 0.00003 |
S | 1116 | T1116T | acT | acC | 3 | 3 | AY.47 | 0.000093 |
S | 1116 | T1116T | acT | acC | 3 | 3 | B.1.258.15 | 0.056604 |
S | 1116 | T1116T | acT | acC | 3 | 3 | B.1.351 | 0.000089 |
S | 1116 | T1116T | acT | acC | 3 | 3 | B.1.367 | 0.002377 |
S | 1116 | T1116T | acT | acC | 3 | 3 | B.1.438.1 | 0.000322 |
S | 1116 | T1116T | acT | acC | 3 | 3 | P.1.2 | 0.003468 |
S | 1116 | T1116T | acT | acC | 2 | 2 | AY.20 | 0.000078 |
S | 1116 | T1116T | acT | acC | 2 | 2 | AY.4.2.1 | 0.000298 |
S | 1116 | T1116T | acT | acC | 2 | 2 | AY.42 | 0.00008 |
S | 1116 | T1116T | acT | acC | 2 | 2 | AY.5 | 0.000041 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.1.153 | 0.002191 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.1.348 | 0.001592 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.1.519 | 0.000079 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.1.70 | 0.000682 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.170 | 0.008621 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.177.44 | 0.001038 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.590 | 0.009091 |
S | 1116 | T1116T | acT | acC | 2 | 2 | B.1.595 | 0.000522 |
S | 1116 | T1116T | acT | acC | 2 | 2 | P.1 | 0.000032 |
S | 1116 | T1116T | acT | acC | 2 | 2 | P.1.6 | 0.003891 |
S | 1116 | T1116T | acT | acC | 1 | 1 | A.2.5 | 0.000499 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AT.1 | 0.005128 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.108 | 0.001103 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.117 | 0.000085 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.29 | 0.000016 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.3.1 | 0.000085 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.33 | 0.000067 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.36 | 0.000148 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.4.2 | 0.000022 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.46.2 | 0.000635 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.54 | 0.000095 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.61 | 0.000105 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.7.2 | 0.000559 |
S | 1116 | T1116T | acT | acC | 1 | 1 | AY.75.1 | 0.00018 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.170 | 0.001247 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.265 | 0.003155 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.277 | 0.000759 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.288 | 0.001916 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.318 | 0.000302 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.37 | 0.000193 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.372 | 0.000689 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.377 | 0.001381 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.398 | 0.003226 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.409 | 0.002833 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.47 | 0.005348 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.1.50 | 0.000679 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.157 | 0.002985 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.177.10 | 0.000878 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.177.12 | 0.000152 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.177.7 | 0.000165 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.177.75 | 0.001041 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.177.81 | 0.000189 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.242 | 0.018868 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.258.16 | 0.001637 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.258.3 | 0.001675 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.293 | 0.0125 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.362 | 0.001541 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.406 | 0.006061 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.425 | 0.002994 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.429 | 0.000024 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.432 | 0.011236 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.473 | 0.019231 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.526 | 0.000024 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.576 | 0.000907 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.596 | 0.000087 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.599 | 0.00365 |
S | 1116 | T1116T | acT | acC | 1 | 1 | B.1.630 | 0.005236 |
S | 1116 | T1116T | acT | acC | 1 | 1 | C.35 | 0.000774 |
S | 1116 | T1116T | acT | acC | 1 | 1 | Q.8 | 0.000165 |
S | 1116 | T1116T | acT | acC | 1 | 1 | Z.1 | 0.00289 |
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
|