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 |
N | 3 | D3E | nonsyn | gaT | gaA | 2404 | 2403 | 0.999584 | 28280-28282 |
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 |
N | 3 | D3E | gaT | gaA | 2403 | 2404 | All | 0.00046 |
N | 3 | D3E | gaT | gaA | 920 | 920 | B.1.1.7 | 0.000824 |
N | 3 | D3E | gaT | gaA | 597 | 597 | B.1.1 | 0.01083 |
N | 3 | D3E | gaT | gaA | 469 | 469 | B.1 | 0.004296 |
N | 3 | D3E | gaT | gaA | 55 | 55 | B.1.177.73 | 0.031144 |
N | 3 | D3E | gaT | gaA | 34 | 34 | B.1.1.409 | 0.096317 |
N | 3 | D3E | gaT | gaA | 21 | 21 | B.1.177 | 0.000277 |
N | 3 | D3E | gaT | gaA | 20 | 20 | B.1.221 | 0.001421 |
N | 3 | D3E | gaT | gaA | 20 | 20 | Q.1 | 0.002527 |
N | 3 | D3E | gaT | gaA | 17 | 17 | B.1.2 | 0.00015 |
N | 3 | D3E | gaT | gaA | 14 | 14 | B.1.375 | 0.011475 |
N | 3 | D3E | gaT | gaA | 13 | 13 | B.1.596 | 0.001133 |
N | 3 | D3E | gaT | gaA | 12 | 12 | B.1.177.7 | 0.001978 |
N | 3 | D3E | gaT | gaA | 11 | 11 | B.1.1.507 | 0.095652 |
N | 3 | D3E | gaT | gaA | 10 | 10 | B.1.1.161 | 0.035336 |
N | 3 | D3E | gaT | gaA | 9 | 9 | AY.43 | 0.00004 |
N | 3 | D3E | gaT | gaA | 9 | 9 | B.1.576 | 0.00816 |
N | 3 | D3E | gaT | gaA | 8 | 8 | AY.25 | 0.000048 |
N | 3 | D3E | gaT | gaA | 8 | 8 | B.1.526 | 0.000188 |
N | 3 | D3E | gaT | gaA | 7 | 7 | B | 0.000895 |
N | 3 | D3E | gaT | gaA | 4 | 5 | B.1.617.2 | 0.000015 |
N | 3 | D3E | gaT | gaA | 4 | 4 | AY.42 | 0.000161 |
N | 3 | D3E | gaT | gaA | 4 | 4 | AY.5 | 0.000083 |
N | 3 | D3E | gaT | gaA | 4 | 4 | B.1.160 | 0.000125 |
N | 3 | D3E | gaT | gaA | 4 | 4 | B.1.258.17 | 0.000416 |
N | 3 | D3E | gaT | gaA | 4 | 4 | Q.3 | 0.00058 |
N | 3 | D3E | gaT | gaA | 3 | 3 | A | 0.001161 |
N | 3 | D3E | gaT | gaA | 3 | 3 | A.2.5 | 0.001497 |
N | 3 | D3E | gaT | gaA | 3 | 3 | AY.4 | 0.000005 |
N | 3 | D3E | gaT | gaA | 3 | 3 | AY.44 | 0.000018 |
N | 3 | D3E | gaT | gaA | 3 | 3 | AY.92 | 0.000862 |
N | 3 | D3E | gaT | gaA | 3 | 3 | B.1.1.519 | 0.000119 |
N | 3 | D3E | gaT | gaA | 3 | 3 | B.1.139 | 0.002199 |
N | 3 | D3E | gaT | gaA | 3 | 3 | B.1.214.2 | 0.001799 |
N | 3 | D3E | gaT | gaA | 3 | 3 | B.1.369 | 0.000856 |
N | 3 | D3E | gaT | gaA | 3 | 3 | B.1.623 | 0.001609 |
N | 3 | D3E | gaT | gaA | 3 | 3 | B.1.637 | 0.000219 |
N | 3 | D3E | gaT | gaA | 3 | 3 | P.1 | 0.000047 |
N | 3 | D3E | gaT | gaA | 3 | 3 | Q.4 | 0.001364 |
N | 3 | D3E | gaT | gaA | 2 | 2 | 0.111111 | |
N | 3 | D3E | gaT | gaA | 2 | 2 | AY.29 | 0.000032 |
N | 3 | D3E | gaT | gaA | 2 | 2 | AY.52 | 0.001629 |
N | 3 | D3E | gaT | gaA | 2 | 2 | AY.75 | 0.000112 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.1.220 | 0.003717 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.1.370 | 0.025316 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.177.86 | 0.000367 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.311 | 0.000549 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.351 | 0.000059 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.397 | 0.009709 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.427 | 0.000101 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.429 | 0.000047 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.580 | 0.00813 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.595 | 0.000522 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.599 | 0.007299 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.621 | 0.000177 |
N | 3 | D3E | gaT | gaA | 2 | 2 | B.1.94 | 0.054054 |
N | 3 | D3E | gaT | gaA | 2 | 2 | P.1.13 | 0.001797 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.103 | 0.000006 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.13 | 0.000161 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.23 | 0.00007 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.34 | 0.000097 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.39.1 | 0.00004 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.4.2 | 0.000022 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.4.5 | 0.000107 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.40 | 0.000964 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.47 | 0.000031 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.71 | 0.000475 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.75.1 | 0.00018 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.9.2 | 0.000037 |
N | 3 | D3E | gaT | gaA | 1 | 1 | AY.95 | 0.000761 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.10 | 0.001115 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.171 | 0.003676 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.216 | 0.00089 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.236 | 0.006897 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.28 | 0.000311 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.348 | 0.000796 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.374 | 0.002375 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.389 | 0.006061 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.464 | 0.001473 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.70 | 0.000341 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.1.99 | 0.02381 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.149 | 0.003425 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.177.21 | 0.000076 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.177.52 | 0.001757 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.177.67 | 0.007634 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.206 | 0.000816 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.234 | 0.000132 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.243 | 0.00007 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.301 | 0.005917 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.399 | 0.001934 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.417 | 0.028571 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.432 | 0.011236 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.433 | 0.003195 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.524 | 0.001406 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.564 | 0.000426 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.565 | 0.00081 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.577 | 0.000687 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.619 | 0.000871 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.620 | 0.000946 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.627 | 0.00202 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.628 | 0.000352 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.634 | 0.003425 |
N | 3 | D3E | gaT | gaA | 1 | 1 | B.1.636 | 0.006711 |
N | 3 | D3E | gaT | gaA | 1 | 1 | P.1.1 | 0.000318 |
N | 3 | D3E | gaT | gaA | 1 | 1 | P.1.10 | 0.000269 |
N | 3 | D3E | gaT | gaA | 1 | 1 | P.1.12 | 0.000484 |
N | 3 | D3E | gaT | gaA | 1 | 1 | P.1.15 | 0.000232 |
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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