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/nsp1 | 3 | S3S | S3S | syn | agC | agT | 2905 | 2905 | 1 | 272-274 |
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/nsp1 | 3 | S3S | agC | agT | 2905 | 2905 | All | 0.000556 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 887 | 887 | B.1.243 | 0.061722 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 532 | 532 | B.1.1.7 | 0.000476 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 309 | 309 | B.1.1.4 | 0.919643 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 196 | 196 | AY.25 | 0.001179 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 65 | 65 | AY.43 | 0.000288 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 65 | 65 | P.1 | 0.001024 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 57 | 57 | B.1.617.2 | 0.000215 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 56 | 56 | AY.4 | 0.000087 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 53 | 53 | AY.9.2 | 0.001947 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 47 | 47 | B.1.2 | 0.000414 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 38 | 38 | B.1 | 0.000348 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 34 | 34 | B.1.1 | 0.000617 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 31 | 31 | B.1.199 | 0.128099 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 29 | 29 | AY.98.1 | 0.001404 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 28 | 28 | AY.33 | 0.00187 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 26 | 26 | AY.3 | 0.000259 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 25 | 25 | AY.44 | 0.000152 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 22 | 22 | B.1.526 | 0.000517 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 21 | 21 | B.1.177 | 0.000277 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 20 | 20 | B.1.1.47 | 0.106952 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 18 | 18 | B.1.621 | 0.001593 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 18 | 18 | P.1.15 | 0.004182 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 17 | 17 | B.1.1.261 | 0.146552 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 14 | 14 | AY.103 | 0.000087 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 14 | 14 | B.1.429 | 0.000329 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 12 | 12 | B.1.1.41 | 0.075949 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 12 | 12 | P.1.10 | 0.003234 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 8 | 8 | AY.34 | 0.000776 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 8 | 8 | B.1.1.63 | 0.003086 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 8 | 8 | B.1.258.16 | 0.013093 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 8 | 8 | B.1.351 | 0.000238 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 7 | 7 | B.1.160 | 0.000218 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 7 | 7 | B.1.258.17 | 0.000728 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 6 | 6 | AY.46.6 | 0.000433 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 6 | 6 | C.37 | 0.000696 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 5 | 5 | AY.20 | 0.000194 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 5 | 5 | AY.26 | 0.000142 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 5 | 5 | AY.29 | 0.000079 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 5 | 5 | AY.9 | 0.000338 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 5 | 5 | AY.99.2 | 0.000461 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 5 | 5 | U.3 | 0.019305 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 4 | 4 | AD.2 | 0.000876 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 4 | 4 | AY.1 | 0.001583 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 4 | 4 | AY.102 | 0.000106 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 4 | 4 | AY.113 | 0.00057 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 4 | 4 | N.9 | 0.02381 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.100 | 0.000138 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.118 | 0.000188 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.119 | 0.000106 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.39 | 0.000074 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.4.2 | 0.000065 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.47 | 0.000093 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.5 | 0.000062 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | AY.98 | 0.000237 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | B.1.146 | 0.012712 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | B.1.221.4 | 0.0125 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | B.1.234 | 0.000396 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | B.1.36 | 0.000438 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | B.1.389 | 0.003006 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | B.1.617.1 | 0.000387 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 3 | 3 | P.2 | 0.00056 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AH.3 | 0.007605 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.16.1 | 0.00094 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.3.1 | 0.000171 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.35 | 0.000466 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.45 | 0.000243 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.54 | 0.000191 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.75 | 0.000112 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | AY.9.1 | 0.000167 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B | 0.000256 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.1.170 | 0.002494 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.1.294 | 0.002532 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.160.30 | 0.005952 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.177.54 | 0.001213 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.177.81 | 0.000379 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.240 | 0.000431 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.369 | 0.00057 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.575 | 0.000607 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.577 | 0.001375 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.582 | 0.000981 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | B.1.637 | 0.000146 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | P.1.14 | 0.000096 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 2 | 2 | Q.8 | 0.00033 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | A.21 | 0.00277 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AA.6 | 0.016129 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AE.8 | 0.000489 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AU.2 | 0.002421 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.10 | 0.00053 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.104 | 0.001984 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.105 | 0.000643 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.109 | 0.00074 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.121 | 0.000135 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.30 | 0.000396 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.51 | 0.000909 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.79 | 0.001211 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.91 | 0.00073 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | AY.99.1 | 0.001553 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.161 | 0.003534 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.207 | 0.001182 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.370 | 0.012658 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.432 | 0.001266 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.434 | 0.000349 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.44 | 0.00241 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.526 | 0.003546 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.111 | 0.001175 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.160.10 | 0.008065 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.177.40 | 0.005155 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.177.42 | 0.000894 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.177.7 | 0.000165 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.239 | 0.001221 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.264.1 | 0.047619 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.329 | 0.000608 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.36.10 | 0.004785 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.36.17 | 0.000494 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.397 | 0.004854 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | B.3 | 0.000831 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | C.30 | 0.001727 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp1 | 3 | S3S | agC | agT | 1 | 1 | Z.1 | 0.00289 |
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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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