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 | 29 | T29T | syn | acT | acC | 1775 | 1721 | 0.969577 | 21647-21649 | |
S | 29 | T29T | syn | acT | acA | 1775 | 50 | 0.028169 | 21647-21649 | |
S | 29 | T29T | syn | acT | acG | 1775 | 4 | 0.00225352 | 21647-21649 |
Details of the mutation T29T 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 | 29 | T29T | acT | acC | 1721 | 1775 | All | 0.000329 |
S | 29 | T29T | acT | acA | 50 | 1775 | All | 0.00001 |
S | 29 | T29T | acT | acG | 4 | 1775 | All | 0.000001 |
S | 29 | T29T | acT | acC | 555 | 555 | AY.43 | 0.002459 |
S | 29 | T29T | acT | acC | 549 | 550 | B.1.617.2 | 0.002067 |
S | 29 | T29T | acT | acA | 1 | 550 | B.1.617.2 | 0.000004 |
S | 29 | T29T | acT | acC | 67 | 76 | B.1.1.7 | 0.00006 |
S | 29 | T29T | acT | acA | 9 | 76 | B.1.1.7 | 0.000008 |
S | 29 | T29T | acT | acC | 71 | 71 | AY.44 | 0.000432 |
S | 29 | T29T | acT | acC | 51 | 53 | AY.4 | 0.000079 |
S | 29 | T29T | acT | acA | 1 | 53 | AY.4 | 0.000002 |
S | 29 | T29T | acT | acG | 1 | 53 | AY.4 | 0.000002 |
S | 29 | T29T | acT | acC | 36 | 36 | AY.39 | 0.00089 |
S | 29 | T29T | acT | acC | 34 | 34 | AY.7 | 0.006664 |
S | 29 | T29T | acT | acA | 27 | 29 | AY.26 | 0.000764 |
S | 29 | T29T | acT | acC | 2 | 29 | AY.26 | 0.000057 |
S | 29 | T29T | acT | acC | 24 | 25 | AY.25 | 0.000144 |
S | 29 | T29T | acT | acA | 1 | 25 | AY.25 | 0.000006 |
S | 29 | T29T | acT | acC | 24 | 24 | B.1.1.207 | 0.028369 |
S | 29 | T29T | acT | acC | 23 | 23 | AY.6 | 0.000946 |
S | 29 | T29T | acT | acC | 14 | 15 | B.1.243 | 0.000974 |
S | 29 | T29T | acT | acA | 1 | 15 | B.1.243 | 0.00007 |
S | 29 | T29T | acT | acC | 14 | 14 | AY.103 | 0.000087 |
S | 29 | T29T | acT | acC | 14 | 14 | AY.118 | 0.000877 |
S | 29 | T29T | acT | acC | 13 | 13 | AY.119 | 0.000459 |
S | 29 | T29T | acT | acC | 10 | 12 | AY.120.1 | 0.00321 |
S | 29 | T29T | acT | acG | 2 | 12 | AY.120.1 | 0.000642 |
S | 29 | T29T | acT | acC | 11 | 11 | AY.102 | 0.000292 |
S | 29 | T29T | acT | acC | 10 | 10 | AY.61 | 0.001048 |
S | 29 | T29T | acT | acC | 9 | 9 | A.2.5 | 0.004491 |
S | 29 | T29T | acT | acC | 9 | 9 | AY.23 | 0.000628 |
S | 29 | T29T | acT | acC | 4 | 9 | B.1 | 0.000037 |
S | 29 | T29T | acT | acA | 4 | 9 | B.1 | 0.000037 |
S | 29 | T29T | acT | acG | 1 | 9 | B.1 | 0.000009 |
S | 29 | T29T | acT | acC | 8 | 8 | AY.111 | 0.001465 |
S | 29 | T29T | acT | acC | 8 | 8 | AY.46 | 0.000833 |
S | 29 | T29T | acT | acC | 8 | 8 | B.1.1.33 | 0.003367 |
S | 29 | T29T | acT | acC | 8 | 8 | P.1 | 0.000126 |
S | 29 | T29T | acT | acC | 7 | 7 | AY.117 | 0.000592 |
S | 29 | T29T | acT | acC | 7 | 7 | B.1.617.1 | 0.000903 |
S | 29 | T29T | acT | acC | 5 | 6 | B.1.177 | 0.000066 |
S | 29 | T29T | acT | acA | 1 | 6 | B.1.177 | 0.000013 |
S | 29 | T29T | acT | acC | 6 | 6 | B.1.177.82 | 0.002864 |
S | 29 | T29T | acT | acC | 6 | 6 | B.1.474 | 0.011407 |
S | 29 | T29T | acT | acC | 5 | 5 | AY.47 | 0.000156 |
S | 29 | T29T | acT | acC | 5 | 5 | AY.5 | 0.000103 |
S | 29 | T29T | acT | acC | 5 | 5 | AY.53 | 0.001438 |
S | 29 | T29T | acT | acC | 4 | 5 | B.1.2 | 0.000035 |
S | 29 | T29T | acT | acA | 1 | 5 | B.1.2 | 0.000009 |
S | 29 | T29T | acT | acC | 5 | 5 | B.1.367 | 0.003962 |
S | 29 | T29T | acT | acC | 3 | 4 | AY.42 | 0.000121 |
S | 29 | T29T | acT | acA | 1 | 4 | AY.42 | 0.00004 |
S | 29 | T29T | acT | acC | 4 | 4 | AY.45 | 0.000487 |
S | 29 | T29T | acT | acC | 4 | 4 | B.1.1 | 0.000073 |
S | 29 | T29T | acT | acC | 4 | 4 | B.1.177.69 | 0.005935 |
S | 29 | T29T | acT | acC | 4 | 4 | B.1.351 | 0.000119 |
S | 29 | T29T | acT | acC | 3 | 3 | AY.34.1 | 0.00153 |
S | 29 | T29T | acT | acC | 3 | 3 | AY.4.5 | 0.000322 |
S | 29 | T29T | acT | acC | 3 | 3 | AY.46.6 | 0.000217 |
S | 29 | T29T | acT | acC | 3 | 3 | B.1.1.526 | 0.010638 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.105 | 0.001286 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.106 | 0.00067 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.120 | 0.000074 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.20 | 0.000078 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.3.1 | 0.000171 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.33 | 0.000134 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.5.3 | 0.000675 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.75 | 0.000112 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.89 | 0.009804 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.9.2 | 0.000073 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.92 | 0.000575 |
S | 29 | T29T | acT | acC | 2 | 2 | AY.98 | 0.000158 |
S | 29 | T29T | acT | acC | 2 | 2 | B.1.110.3 | 0.001437 |
S | 29 | T29T | acT | acA | 1 | 1 | A.2.4 | 0.003367 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.100 | 0.000046 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.110 | 0.000113 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.14 | 0.000088 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.23.1 | 0.000417 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.4.2 | 0.000022 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.46.2 | 0.000635 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.5.4 | 0.000277 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.52 | 0.000814 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.54 | 0.000095 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.58 | 0.000907 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.62 | 0.000436 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.67 | 0.000464 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.68 | 0.000274 |
S | 29 | T29T | acT | acC | 1 | 1 | AY.96 | 0.002075 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.1.214 | 0.000055 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.1.25 | 0.000569 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.1.411 | 0.014706 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.1.519 | 0.00004 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.142 | 0.002899 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.177.15 | 0.000631 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.177.19 | 0.001431 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.177.73 | 0.000566 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.232 | 0.000537 |
S | 29 | T29T | acT | acA | 1 | 1 | B.1.326 | 0.007576 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.36.31 | 0.001751 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.400 | 0.000429 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.429 | 0.000024 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.433 | 0.003195 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.561 | 0.000397 |
S | 29 | T29T | acT | acC | 1 | 1 | B.1.564.1 | 0.001577 |
S | 29 | T29T | acT | acC | 1 | 1 | C.36.3 | 0.000567 |
S | 29 | T29T | acT | acC | 1 | 1 | C.37 | 0.000116 |
S | 29 | T29T | acT | acA | 1 | 1 | D.2 | 0.000075 |
S | 29 | T29T | acT | acC | 1 | 1 | P.1.10.1 | 0.00813 |
S | 29 | T29T | acT | acC | 1 | 1 | Q.1 | 0.000126 |
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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