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 | 1252 | S1252F | nonsyn | tCc | tTc | 7375 | 7374 | 0.999864 | 25316-25318 |
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 |
S | 1252 | S1252F | tCc | tTc | 7374 | 7375 | All | 0.00141 |
S | 1252 | S1252F | tCc | tTc | 1696 | 1696 | P.1.14 | 0.081071 |
S | 1252 | S1252F | tCc | tTc | 1150 | 1150 | AY.71 | 0.546318 |
S | 1252 | S1252F | tCc | tTc | 1063 | 1063 | B.1.427 | 0.053679 |
S | 1252 | S1252F | tCc | tTc | 901 | 901 | AY.4 | 0.001402 |
S | 1252 | S1252F | tCc | tTc | 709 | 709 | B.1.221 | 0.050362 |
S | 1252 | S1252F | tCc | tTc | 523 | 523 | B.1.1.7 | 0.000468 |
S | 1252 | S1252F | tCc | tTc | 188 | 188 | B.1.526 | 0.004419 |
S | 1252 | S1252F | tCc | tTc | 122 | 122 | B.1 | 0.001117 |
S | 1252 | S1252F | tCc | tTc | 114 | 114 | AY.44 | 0.000694 |
S | 1252 | S1252F | tCc | tTc | 99 | 99 | B.1.2 | 0.000872 |
S | 1252 | S1252F | tCc | tTc | 58 | 58 | C.36.1 | 0.240664 |
S | 1252 | S1252F | tCc | tTc | 48 | 48 | AY.5.4 | 0.013282 |
S | 1252 | S1252F | tCc | tTc | 46 | 46 | AY.103 | 0.000286 |
S | 1252 | S1252F | tCc | tTc | 41 | 41 | B.1.429 | 0.000965 |
S | 1252 | S1252F | tCc | tTc | 38 | 38 | B.1.258 | 0.002529 |
S | 1252 | S1252F | tCc | tTc | 38 | 38 | B.1.497 | 0.011961 |
S | 1252 | S1252F | tCc | tTc | 30 | 30 | AY.25 | 0.00018 |
S | 1252 | S1252F | tCc | tTc | 28 | 28 | B.1.617.2 | 0.000105 |
S | 1252 | S1252F | tCc | tTc | 26 | 26 | B.1.177 | 0.000342 |
S | 1252 | S1252F | tCc | tTc | 24 | 24 | P.1 | 0.000378 |
S | 1252 | S1252F | tCc | tTc | 22 | 22 | B.1.351 | 0.000654 |
S | 1252 | S1252F | tCc | tTc | 20 | 20 | AY.43 | 0.000089 |
S | 1252 | S1252F | tCc | tTc | 17 | 17 | AY.20 | 0.000661 |
S | 1252 | S1252F | tCc | tTc | 17 | 17 | B.1.1.263 | 0.02648 |
S | 1252 | S1252F | tCc | tTc | 17 | 17 | B.1.1.306 | 0.007453 |
S | 1252 | S1252F | tCc | tTc | 16 | 16 | B.1.1 | 0.00029 |
S | 1252 | S1252F | tCc | tTc | 14 | 14 | AY.5 | 0.000289 |
S | 1252 | S1252F | tCc | tTc | 12 | 13 | B.1.160 | 0.000374 |
S | 1252 | S1252F | tCc | tTc | 11 | 11 | AY.9.2 | 0.000404 |
S | 1252 | S1252F | tCc | tTc | 11 | 11 | B.1.1.519 | 0.000437 |
S | 1252 | S1252F | tCc | tTc | 10 | 10 | AY.6 | 0.000411 |
S | 1252 | S1252F | tCc | tTc | 9 | 9 | B.1.596 | 0.000784 |
S | 1252 | S1252F | tCc | tTc | 8 | 8 | AY.3 | 0.00008 |
S | 1252 | S1252F | tCc | tTc | 8 | 8 | B.1.311 | 0.002197 |
S | 1252 | S1252F | tCc | tTc | 8 | 8 | B.1.369 | 0.002282 |
S | 1252 | S1252F | tCc | tTc | 7 | 7 | AY.26 | 0.000198 |
S | 1252 | S1252F | tCc | tTc | 7 | 7 | B.1.621 | 0.00062 |
S | 1252 | S1252F | tCc | tTc | 7 | 7 | C.36.3 | 0.003971 |
S | 1252 | S1252F | tCc | tTc | 7 | 7 | P.1.15 | 0.001626 |
S | 1252 | S1252F | tCc | tTc | 6 | 6 | AY.113 | 0.000854 |
S | 1252 | S1252F | tCc | tTc | 6 | 6 | AY.47 | 0.000187 |
S | 1252 | S1252F | tCc | tTc | 6 | 6 | B.1.582 | 0.002944 |
S | 1252 | S1252F | tCc | tTc | 5 | 5 | B.1.1.37 | 0.000964 |
S | 1252 | S1252F | tCc | tTc | 5 | 5 | B.1.177.43 | 0.007386 |
S | 1252 | S1252F | tCc | tTc | 5 | 5 | B.40 | 0.001821 |
S | 1252 | S1252F | tCc | tTc | 5 | 5 | C.36 | 0.004554 |
S | 1252 | S1252F | tCc | tTc | 4 | 4 | AY.13 | 0.000644 |
S | 1252 | S1252F | tCc | tTc | 4 | 4 | AY.38 | 0.001997 |
S | 1252 | S1252F | tCc | tTc | 4 | 4 | B | 0.000511 |
S | 1252 | S1252F | tCc | tTc | 4 | 4 | B.1.234 | 0.000528 |
S | 1252 | S1252F | tCc | tTc | 4 | 4 | B.1.336 | 0.009756 |
S | 1252 | S1252F | tCc | tTc | 4 | 4 | B.1.396 | 0.002823 |
S | 1252 | S1252F | tCc | tTc | 4 | 4 | B.1.525 | 0.000453 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | AY.23 | 0.000209 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | AY.29 | 0.000047 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | AY.39 | 0.000074 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | AY.39.1 | 0.000119 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | AY.42 | 0.000121 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | B.1.1.317 | 0.001235 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | B.1.177.60 | 0.000655 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | B.1.240 | 0.000647 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | B.1.575.1 | 0.007317 |
S | 1252 | S1252F | tCc | tTc | 3 | 3 | B.1.617.1 | 0.000387 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.117 | 0.000169 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.119 | 0.000071 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.3.1 | 0.000171 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.32 | 0.001065 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.33 | 0.000134 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.4.2.1 | 0.000298 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.4.5 | 0.000215 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.41 | 0.000588 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.45 | 0.000243 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.46.3 | 0.001867 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.53 | 0.000575 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.54 | 0.000191 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.59 | 0.001059 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.65 | 0.001066 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.75 | 0.000112 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | AY.85 | 0.000854 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.1.222 | 0.000408 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.1.434 | 0.000697 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.1.62 | 0.054054 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.1.70 | 0.000682 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.146 | 0.008475 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.177.6 | 0.001953 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.177.82 | 0.000955 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.243 | 0.000139 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.258.18 | 0.2 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.375 | 0.001639 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.521 | 0.00995 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | B.1.575 | 0.000607 |
S | 1252 | S1252F | tCc | tTc | 2 | 2 | C.37 | 0.000232 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | A.21 | 0.00277 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AD.2 | 0.000219 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AE.8 | 0.000489 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AH.3 | 0.003802 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.114 | 0.000231 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.118 | 0.000063 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.4.2 | 0.000022 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.4.3 | 0.000842 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.46 | 0.000104 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.56 | 0.001605 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.61 | 0.000105 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.69 | 0.000187 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.7.1 | 0.000113 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.74 | 0.000116 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.9 | 0.000068 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.9.1 | 0.000084 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.94 | 0.000443 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.96 | 0.002075 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | AY.98.1 | 0.000048 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.1.25 | 0.000569 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.1.269 | 0.001353 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.1.28 | 0.000311 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.1.298 | 0.000862 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.1.300 | 0.010753 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.1.366 | 0.015873 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.1.420 | 0.001006 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.177.15 | 0.000631 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.177.17 | 0.000821 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.205 | 0.02381 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.258.17 | 0.000104 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.265 | 0.001271 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.298 | 0.002114 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.351.2 | 0.000303 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.351.5 | 0.0006 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.36 | 0.000146 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.36.29 | 0.000517 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.36.39 | 0.002217 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.428 | 0.00102 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.561 | 0.000397 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.567 | 0.003333 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.576 | 0.000907 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.595 | 0.000261 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.596.1 | 0.009346 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.609 | 0.000479 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.631 | 0.003367 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | B.1.9.5 | 0.005682 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | C.16 | 0.00106 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | P.2 | 0.000187 |
S | 1252 | S1252F | tCc | tTc | 1 | 1 | P.3 | 0.001595 |
S | 1252 | S1252F | tCc | tTc | 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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