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 | 575 | A575S | nonsyn | Gct | Tct | 1651 | 1645 | 0.996366 | 23285-23287 | |
S | 575 | A575S | nonsyn | GcT | TcC | 1651 | 4 | 0.00242277 | 23285-23287 | |
S | 575 | A575S | nonsyn | GCt | AGt | 1651 | 2 | 0.00121139 | 23285-23287 |
Details of the mutation A575S 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 | 575 | A575S | Gct | Tct | 1645 | 1651 | All | 0.000315 |
S | 575 | A575S | GcT | TcC | 4 | 1651 | All | 0.000001 |
S | 575 | A575S | GCt | AGt | 2 | 1651 | All | 0 |
S | 575 | A575S | Gct | Tct | 612 | 612 | B.1.1.7 | 0.000548 |
S | 575 | A575S | Gct | Tct | 177 | 177 | B.1.2 | 0.001559 |
S | 575 | A575S | Gct | Tct | 67 | 67 | AY.4 | 0.000104 |
S | 575 | A575S | Gct | Tct | 58 | 58 | B.1.240 | 0.012503 |
S | 575 | A575S | Gct | Tct | 54 | 54 | B.1.1 | 0.00098 |
S | 575 | A575S | Gct | Tct | 51 | 51 | B.1 | 0.000467 |
S | 575 | A575S | Gct | Tct | 39 | 39 | B.1.617.2 | 0.000147 |
S | 575 | A575S | Gct | Tct | 32 | 32 | AY.120 | 0.00119 |
S | 575 | A575S | Gct | Tct | 30 | 30 | B.1.36 | 0.004377 |
S | 575 | A575S | Gct | Tct | 27 | 27 | C.37 | 0.003134 |
S | 575 | A575S | Gct | Tct | 26 | 26 | B.1.1.50 | 0.017651 |
S | 575 | A575S | Gct | Tct | 25 | 25 | B.1.160.28 | 0.073099 |
S | 575 | A575S | Gct | Tct | 22 | 22 | B.1.160 | 0.000686 |
S | 575 | A575S | Gct | Tct | 21 | 21 | B.1.1.222 | 0.004284 |
S | 575 | A575S | Gct | Tct | 18 | 18 | AY.119 | 0.000636 |
S | 575 | A575S | Gct | Tct | 15 | 15 | AY.102 | 0.000398 |
S | 575 | A575S | Gct | Tct | 15 | 15 | AY.117 | 0.001268 |
S | 575 | A575S | Gct | Tct | 14 | 14 | B.1.177.57 | 0.003934 |
S | 575 | A575S | Gct | Tct | 14 | 14 | B.1.429 | 0.000329 |
S | 575 | A575S | Gct | Tct | 13 | 13 | AY.33 | 0.000868 |
S | 575 | A575S | Gct | Tct | 13 | 13 | AY.44 | 0.000079 |
S | 575 | A575S | Gct | Tct | 12 | 12 | AY.43 | 0.000053 |
S | 575 | A575S | Gct | Tct | 12 | 12 | B.1.351 | 0.000357 |
S | 575 | A575S | Gct | Tct | 11 | 11 | B.1.221 | 0.000781 |
S | 575 | A575S | Gct | Tct | 11 | 11 | B.1.298 | 0.023256 |
S | 575 | A575S | Gct | Tct | 10 | 10 | AY.3 | 0.000099 |
S | 575 | A575S | Gct | Tct | 10 | 10 | AY.34 | 0.00097 |
S | 575 | A575S | Gct | Tct | 10 | 10 | B.1.1.519 | 0.000397 |
S | 575 | A575S | Gct | Tct | 9 | 9 | AY.25 | 0.000054 |
S | 575 | A575S | Gct | Tct | 9 | 9 | AY.5 | 0.000186 |
S | 575 | A575S | Gct | Tct | 9 | 9 | B.1.1.284 | 0.000967 |
S | 575 | A575S | Gct | Tct | 8 | 9 | D.2 | 0.0006 |
S | 575 | A575S | GCt | AGt | 1 | 9 | D.2 | 0.000075 |
S | 575 | A575S | Gct | Tct | 8 | 8 | P.2 | 0.001493 |
S | 575 | A575S | Gct | Tct | 7 | 7 | B.1.36.1 | 0.007982 |
S | 575 | A575S | Gct | Tct | 7 | 7 | B.1.595 | 0.001827 |
S | 575 | A575S | Gct | Tct | 6 | 6 | AY.100 | 0.000276 |
S | 575 | A575S | Gct | Tct | 6 | 6 | B.1.177 | 0.000079 |
S | 575 | A575S | Gct | Tct | 6 | 6 | R.1 | 0.00054 |
S | 575 | A575S | Gct | Tct | 5 | 5 | AY.103 | 0.000031 |
S | 575 | A575S | Gct | Tct | 5 | 5 | AY.4.2 | 0.000108 |
S | 575 | A575S | Gct | Tct | 5 | 5 | B.1.427 | 0.000252 |
S | 575 | A575S | Gct | Tct | 5 | 5 | B.1.526 | 0.000118 |
S | 575 | A575S | Gct | Tct | 5 | 5 | B.4.7 | 0.050505 |
S | 575 | A575S | Gct | Tct | 4 | 4 | B.1.1.28 | 0.001245 |
S | 575 | A575S | GcT | TcC | 4 | 4 | B.1.1.318 | 0.001207 |
S | 575 | A575S | Gct | Tct | 4 | 4 | B.1.617.1 | 0.000516 |
S | 575 | A575S | Gct | Tct | 4 | 4 | P.1 | 0.000063 |
S | 575 | A575S | Gct | Tct | 3 | 3 | A | 0.001161 |
S | 575 | A575S | Gct | Tct | 3 | 3 | AY.35 | 0.000699 |
S | 575 | A575S | Gct | Tct | 3 | 3 | AY.42 | 0.000121 |
S | 575 | A575S | Gct | Tct | 3 | 3 | AY.61 | 0.000314 |
S | 575 | A575S | Gct | Tct | 3 | 3 | B.1.258 | 0.0002 |
S | 575 | A575S | Gct | Tct | 3 | 3 | B.1.619 | 0.002613 |
S | 575 | A575S | Gct | Tct | 3 | 3 | P.1.14 | 0.000143 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.23 | 0.000139 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.29.1 | 0.000441 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.3.1 | 0.000171 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.39 | 0.000049 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.4.3 | 0.001684 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.46.4 | 0.000329 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.74 | 0.000231 |
S | 575 | A575S | Gct | Tct | 2 | 2 | AY.75 | 0.000112 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.1.10 | 0.00223 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.1.192 | 0.004619 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.177.21 | 0.000153 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.234 | 0.000264 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.36.8 | 0.002 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.456 | 0.006536 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.466.2 | 0.000782 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.525 | 0.000226 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.596 | 0.000174 |
S | 575 | A575S | Gct | Tct | 2 | 2 | B.1.621 | 0.000177 |
S | 575 | A575S | Gct | Tct | 1 | 1 | A.1 | 0.000282 |
S | 575 | A575S | Gct | Tct | 1 | 1 | A.19 | 0.009434 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.108 | 0.001103 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.118 | 0.000063 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.121 | 0.000135 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.29 | 0.000016 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.4.5 | 0.000107 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.47 | 0.000031 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.5.2 | 0.002463 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.5.3 | 0.000337 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.53 | 0.000288 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.6 | 0.000041 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.7.2 | 0.000559 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.78 | 0.001541 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.81 | 0.001992 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.9.2 | 0.000037 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.90 | 0.000684 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.92 | 0.000287 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.93 | 0.000273 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.98 | 0.000079 |
S | 575 | A575S | Gct | Tct | 1 | 1 | AY.99.2 | 0.000092 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B | 0.000128 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.141 | 0.002012 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.176 | 0.000439 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.208 | 0.012195 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.214 | 0.000055 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.266 | 0.012195 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.311 | 0.000358 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.33 | 0.000421 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.34 | 0.013158 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.37 | 0.000193 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.398 | 0.003226 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.428 | 0.009434 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.434 | 0.000349 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.52 | 0.012195 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.1.528 | 0.004808 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.128 | 0.000635 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.177.35 | 0.000691 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.223 | 0.002778 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.224 | 0.025 |
S | 575 | A575S | GCt | AGt | 1 | 1 | B.1.243 | 0.00007 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.3 | 0.002618 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.324 | 0.001605 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.351.2 | 0.000303 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.36.10 | 0.004785 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.361 | 0.001289 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.363 | 0.012987 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.409 | 0.000781 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.459 | 0.004082 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.1.627 | 0.00202 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.4.1 | 0.018868 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.40 | 0.000364 |
S | 575 | A575S | Gct | Tct | 1 | 1 | B.6.6 | 0.000889 |
S | 575 | A575S | Gct | Tct | 1 | 1 | K.2 | 0.04 |
S | 575 | A575S | Gct | Tct | 1 | 1 | P.1.16 | 0.000374 |
S | 575 | A575S | Gct | Tct | 1 | 1 | Q.1 | 0.000126 |
S | 575 | A575S | Gct | Tct | 1 | 1 | Q.3 | 0.000145 |
S | 575 | A575S | Gct | Tct | 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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