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 | 144 | D144D | syn | gaT | gaC | 2641 | 2641 | 1 | 28703-28705 |
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 | 144 | D144D | gaT | gaC | 2641 | 2641 | All | 0.000505 |
N | 144 | D144D | gaT | gaC | 557 | 557 | P.1 | 0.008775 |
N | 144 | D144D | gaT | gaC | 492 | 492 | B.1.1.7 | 0.00044 |
N | 144 | D144D | gaT | gaC | 475 | 475 | AY.39.1 | 0.018816 |
N | 144 | D144D | gaT | gaC | 174 | 174 | B.1.2 | 0.001532 |
N | 144 | D144D | gaT | gaC | 125 | 125 | AY.4 | 0.000195 |
N | 144 | D144D | gaT | gaC | 82 | 82 | AY.73 | 0.054558 |
N | 144 | D144D | gaT | gaC | 60 | 60 | AY.47 | 0.001866 |
N | 144 | D144D | gaT | gaC | 59 | 59 | B.1.427 | 0.002979 |
N | 144 | D144D | gaT | gaC | 47 | 47 | B.1.617.2 | 0.000177 |
N | 144 | D144D | gaT | gaC | 44 | 44 | AY.43 | 0.000195 |
N | 144 | D144D | gaT | gaC | 40 | 40 | B.1.568 | 0.044444 |
N | 144 | D144D | gaT | gaC | 39 | 39 | B.1.91 | 0.080913 |
N | 144 | D144D | gaT | gaC | 15 | 15 | AY.103 | 0.000093 |
N | 144 | D144D | gaT | gaC | 15 | 15 | B.1 | 0.000137 |
N | 144 | D144D | gaT | gaC | 15 | 15 | B.1.243 | 0.001044 |
N | 144 | D144D | gaT | gaC | 14 | 14 | A.2 | 0.009265 |
N | 144 | D144D | gaT | gaC | 13 | 13 | AY.25 | 0.000078 |
N | 144 | D144D | gaT | gaC | 13 | 13 | B.1.1 | 0.000236 |
N | 144 | D144D | gaT | gaC | 13 | 13 | B.1.160 | 0.000405 |
N | 144 | D144D | gaT | gaC | 13 | 13 | B.1.450 | 0.147727 |
N | 144 | D144D | gaT | gaC | 12 | 12 | AY.120 | 0.000446 |
N | 144 | D144D | gaT | gaC | 12 | 12 | AY.44 | 0.000073 |
N | 144 | D144D | gaT | gaC | 11 | 11 | B.1.526 | 0.000259 |
N | 144 | D144D | gaT | gaC | 10 | 10 | B.1.351 | 0.000297 |
N | 144 | D144D | gaT | gaC | 9 | 9 | C.37 | 0.001045 |
N | 144 | D144D | gaT | gaC | 8 | 8 | AY.3 | 0.00008 |
N | 144 | D144D | gaT | gaC | 8 | 8 | AY.45 | 0.000973 |
N | 144 | D144D | gaT | gaC | 7 | 7 | AY.106 | 0.002344 |
N | 144 | D144D | gaT | gaC | 7 | 7 | AY.26 | 0.000198 |
N | 144 | D144D | gaT | gaC | 7 | 7 | AY.4.4 | 0.002864 |
N | 144 | D144D | gaT | gaC | 7 | 7 | B.1.1.306 | 0.003069 |
N | 144 | D144D | gaT | gaC | 7 | 7 | B.1.36 | 0.001021 |
N | 144 | D144D | gaT | gaC | 7 | 7 | B.1.525 | 0.000792 |
N | 144 | D144D | gaT | gaC | 7 | 7 | B.1.621 | 0.00062 |
N | 144 | D144D | gaT | gaC | 7 | 7 | P.1.14 | 0.000335 |
N | 144 | D144D | gaT | gaC | 6 | 6 | AY.20 | 0.000233 |
N | 144 | D144D | gaT | gaC | 6 | 6 | AY.34 | 0.000582 |
N | 144 | D144D | gaT | gaC | 6 | 6 | AY.39 | 0.000148 |
N | 144 | D144D | gaT | gaC | 6 | 6 | AY.4.2.1 | 0.000894 |
N | 144 | D144D | gaT | gaC | 6 | 6 | B.1.177.57 | 0.001686 |
N | 144 | D144D | gaT | gaC | 6 | 6 | B.1.351.2 | 0.001815 |
N | 144 | D144D | gaT | gaC | 6 | 6 | B.1.596 | 0.000523 |
N | 144 | D144D | gaT | gaC | 5 | 5 | AY.5 | 0.000103 |
N | 144 | D144D | gaT | gaC | 5 | 5 | B.1.1.33 | 0.002104 |
N | 144 | D144D | gaT | gaC | 5 | 5 | B.1.492 | 0.035211 |
N | 144 | D144D | gaT | gaC | 5 | 5 | B.1.565 | 0.004052 |
N | 144 | D144D | gaT | gaC | 5 | 5 | B.1.617.1 | 0.000645 |
N | 144 | D144D | gaT | gaC | 5 | 5 | D.2 | 0.000375 |
N | 144 | D144D | gaT | gaC | 5 | 5 | P.1.12 | 0.00242 |
N | 144 | D144D | gaT | gaC | 4 | 4 | AY.9 | 0.00027 |
N | 144 | D144D | gaT | gaC | 4 | 4 | B.1.1.519 | 0.000159 |
N | 144 | D144D | gaT | gaC | 4 | 4 | B.1.177.52 | 0.00703 |
N | 144 | D144D | gaT | gaC | 4 | 4 | B.1.429 | 0.000094 |
N | 144 | D144D | gaT | gaC | 4 | 4 | P.1.15 | 0.000929 |
N | 144 | D144D | gaT | gaC | 3 | 3 | A.2.5 | 0.001497 |
N | 144 | D144D | gaT | gaC | 3 | 3 | AY.16 | 0.001139 |
N | 144 | D144D | gaT | gaC | 3 | 3 | AY.29 | 0.000047 |
N | 144 | D144D | gaT | gaC | 3 | 3 | AY.53 | 0.000863 |
N | 144 | D144D | gaT | gaC | 3 | 3 | AY.9.2 | 0.00011 |
N | 144 | D144D | gaT | gaC | 3 | 3 | B.1.1.214 | 0.000166 |
N | 144 | D144D | gaT | gaC | 3 | 3 | B.1.177 | 0.00004 |
N | 144 | D144D | gaT | gaC | 3 | 3 | B.1.311 | 0.000824 |
N | 144 | D144D | gaT | gaC | 3 | 3 | B.1.36.8 | 0.003 |
N | 144 | D144D | gaT | gaC | 3 | 3 | P.2 | 0.00056 |
N | 144 | D144D | gaT | gaC | 2 | 2 | AM.4 | 0.007143 |
N | 144 | D144D | gaT | gaC | 2 | 2 | AY.109 | 0.001479 |
N | 144 | D144D | gaT | gaC | 2 | 2 | AY.117 | 0.000169 |
N | 144 | D144D | gaT | gaC | 2 | 2 | AY.119 | 0.000071 |
N | 144 | D144D | gaT | gaC | 2 | 2 | AY.120.1 | 0.000642 |
N | 144 | D144D | gaT | gaC | 2 | 2 | AY.61 | 0.00021 |
N | 144 | D144D | gaT | gaC | 2 | 2 | AY.99 | 0.002099 |
N | 144 | D144D | gaT | gaC | 2 | 2 | B.1.1.280 | 0.006173 |
N | 144 | D144D | gaT | gaC | 2 | 2 | B.1.1.354 | 0.008772 |
N | 144 | D144D | gaT | gaC | 2 | 2 | B.1.1.39 | 0.001019 |
N | 144 | D144D | gaT | gaC | 2 | 2 | B.1.398 | 0.005952 |
N | 144 | D144D | gaT | gaC | 2 | 2 | B.1.453 | 0.006472 |
N | 144 | D144D | gaT | gaC | 2 | 2 | P.1.10 | 0.000539 |
N | 144 | D144D | gaT | gaC | 2 | 2 | P.1.17 | 0.000324 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.102 | 0.000027 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.111 | 0.000183 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.115 | 0.005208 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.12 | 0.000316 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.13 | 0.000161 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.14 | 0.000088 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.16.1 | 0.00047 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.19 | 0.00114 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.24 | 0.000431 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.30 | 0.000396 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.4.5 | 0.000107 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.46.6 | 0.000072 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.54 | 0.000095 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.6 | 0.000041 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.65 | 0.000533 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.69 | 0.000187 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.74 | 0.000116 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.75.1 | 0.00018 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.77 | 0.001127 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.90 | 0.000684 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.91 | 0.00073 |
N | 144 | D144D | gaT | gaC | 1 | 1 | AY.98.1 | 0.000048 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.152 | 0.04 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.220 | 0.001859 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.222 | 0.000204 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.231 | 0.003096 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.284 | 0.000107 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.291 | 0.000742 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.311 | 0.000358 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.322 | 0.008772 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.326 | 0.001761 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.353 | 0.020833 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.41 | 0.006329 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.51 | 0.001718 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.1.70 | 0.000341 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.177.20 | 0.001517 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.177.6 | 0.000977 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.177.81 | 0.000189 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.177.82 | 0.000477 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.210 | 0.002132 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.221 | 0.000071 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.258 | 0.000067 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.350 | 0.002933 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.356 | 0.001727 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.396 | 0.000706 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.466.2 | 0.000391 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.497 | 0.000315 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.582 | 0.000491 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.612 | 0.002653 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.619.1 | 0.000641 |
N | 144 | D144D | gaT | gaC | 1 | 1 | B.1.637 | 0.000073 |
N | 144 | D144D | gaT | gaC | 1 | 1 | P.1.1 | 0.000318 |
N | 144 | D144D | gaT | gaC | 1 | 1 | Q.1 | 0.000126 |
N | 144 | D144D | gaT | gaC | 1 | 1 | Q.7 | 0.001111 |
N | 144 | D144D | gaT | gaC | 1 | 1 | R.1 | 0.00009 |
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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