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 | 169 | P169S | P4561S | nonsyn | Cca | Tca | 1128 | 1126 | 0.998227 | 13945-13947 |
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 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1126 | 1128 | All | 0.000215 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 245 | 245 | AY.5 | 0.005059 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 155 | 155 | B.1.617.2 | 0.000584 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 125 | 125 | AY.4 | 0.000195 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 74 | 74 | B.1.1.7 | 0.000066 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 51 | 51 | AY.20 | 0.001982 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 45 | 45 | XA | 1 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 42 | 42 | AY.43 | 0.000186 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 32 | 32 | B.1.221 | 0.002273 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 32 | 32 | B.1.239 | 0.039072 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 27 | 27 | B.1.177.18 | 0.031323 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 23 | 23 | B.1.1.214 | 0.001276 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 22 | 22 | AY.44 | 0.000134 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 20 | 20 | AY.46.5 | 0.003968 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 15 | 15 | B.1.2 | 0.000132 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 14 | 14 | B.1 | 0.000128 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 13 | 13 | AY.39 | 0.000321 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 12 | 12 | AY.102 | 0.000318 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 9 | 9 | AY.34 | 0.000873 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 9 | 9 | AY.7.2 | 0.005034 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 8 | 8 | AY.25 | 0.000048 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 8 | 8 | B.1.525 | 0.000905 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 7 | 7 | B.1.177 | 0.000092 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 4 | 6 | 0.222222 | |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 5 | 5 | AY.103 | 0.000031 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 5 | 5 | AY.106 | 0.001674 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 5 | 5 | B.1.1.222 | 0.00102 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 5 | 5 | B.1.1.398 | 0.016129 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 5 | 5 | B.1.429 | 0.000118 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 4 | 4 | AY.100 | 0.000184 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 4 | 4 | AY.24 | 0.001724 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 4 | 4 | AY.36 | 0.000593 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 4 | 4 | B.1.9 | 0.024691 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 4 | 4 | P.1.16 | 0.001496 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | AY.46 | 0.000312 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | AY.98 | 0.000237 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | B | 0.000383 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | B.1.1.519 | 0.000119 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | B.1.258.17 | 0.000312 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | B.1.526 | 0.000071 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 3 | 3 | B.1.621 | 0.000266 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | AY.5.4 | 0.000553 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | AY.6 | 0.000082 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | AY.95 | 0.001522 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | B.1.1.47 | 0.010695 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | B.1.243 | 0.000139 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | B.1.597 | 0.009259 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | P.1.10 | 0.000539 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 2 | 2 | Q.8 | 0.00033 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | A | 0.000387 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | A.5 | 0.001923 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.30 | 0.000396 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.37 | 0.000316 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.46.4 | 0.000165 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.59 | 0.00053 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.8 | 0.000606 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.1.153 | 0.001095 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.1.284 | 0.000107 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.1.318 | 0.000302 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.1.326 | 0.001761 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.1.33 | 0.000421 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.1.434 | 0.000349 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.241 | 0.000812 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.351.3 | 0.000876 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.36.29 | 0.000517 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.380 | 0.006623 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.524 | 0.001406 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.575 | 0.000303 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.587 | 0.001898 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.1.619 | 0.000871 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | B.4.1 | 0.018868 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | C.1 | 0.002392 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | C.14 | 0.004329 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | C.30 | 0.001727 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | C.37 | 0.000116 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp12 | 169 | P169S | Cca | Tca | 1 | 1 | Q.3 | 0.000145 |
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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