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 | 25 | P25L | nonsyn | cCc | cTc | 1574 | 1566 | 0.994917 | 21635-21637 | |
S | 25 | P25L | nonsyn | cCC | cTT | 1574 | 5 | 0.00317662 | 21635-21637 | |
S | 25 | P25L | nonsyn | cCC | cTA | 1574 | 2 | 0.00127065 | 21635-21637 | |
S | 25 | P25L | nonsyn | CCC | TTA | 1574 | 1 | 0.000635324 | 21635-21637 |
Details of the mutation P25L 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 | 25 | P25L | cCc | cTc | 1566 | 1574 | All | 0.0003 |
S | 25 | P25L | cCC | cTT | 5 | 1574 | All | 0.000001 |
S | 25 | P25L | cCC | cTA | 2 | 1574 | All | 0 |
S | 25 | P25L | CCC | TTA | 1 | 1574 | All | 0 |
S | 25 | P25L | cCc | cTc | 417 | 418 | B.1.1.7 | 0.000373 |
S | 25 | P25L | CCC | TTA | 1 | 418 | B.1.1.7 | 0.000001 |
S | 25 | P25L | cCc | cTc | 195 | 195 | AY.4 | 0.000304 |
S | 25 | P25L | cCc | cTc | 116 | 116 | C.1.2 | 0.493617 |
S | 25 | P25L | cCc | cTc | 87 | 87 | B.1.160 | 0.002713 |
S | 25 | P25L | cCc | cTc | 55 | 55 | B.1.351 | 0.001635 |
S | 25 | P25L | cCc | cTc | 45 | 45 | B.1.617.2 | 0.000169 |
S | 25 | P25L | cCc | cTc | 40 | 40 | AY.43 | 0.000177 |
S | 25 | P25L | cCc | cTc | 32 | 32 | AY.103 | 0.000199 |
S | 25 | P25L | cCc | cTc | 32 | 32 | AY.25 | 0.000192 |
S | 25 | P25L | cCc | cTc | 31 | 31 | AY.44 | 0.000189 |
S | 25 | P25L | cCc | cTc | 30 | 30 | B.1.2 | 0.000264 |
S | 25 | P25L | cCc | cTc | 28 | 28 | AY.120 | 0.001041 |
S | 25 | P25L | cCc | cTc | 28 | 28 | AY.20 | 0.001088 |
S | 25 | P25L | cCc | cTc | 21 | 21 | B.1.177 | 0.000277 |
S | 25 | P25L | cCc | cTc | 20 | 20 | AY.45 | 0.002434 |
S | 25 | P25L | cCc | cTc | 18 | 18 | B.1 | 0.000165 |
S | 25 | P25L | cCc | cTc | 15 | 15 | AY.29 | 0.000237 |
S | 25 | P25L | cCc | cTc | 15 | 15 | B.1.214.2 | 0.008993 |
S | 25 | P25L | cCc | cTc | 15 | 15 | P.1 | 0.000236 |
S | 25 | P25L | cCc | cTc | 14 | 14 | C.36.3.1 | 0.038043 |
S | 25 | P25L | cCc | cTc | 13 | 13 | B.1.1 | 0.000236 |
S | 25 | P25L | cCc | cTc | 12 | 12 | AY.3 | 0.000119 |
S | 25 | P25L | cCc | cTc | 12 | 12 | B.1.1.63 | 0.00463 |
S | 25 | P25L | cCc | cTc | 11 | 11 | AY.3.1 | 0.000938 |
S | 25 | P25L | cCc | cTc | 10 | 10 | AY.102 | 0.000265 |
S | 25 | P25L | cCc | cTc | 9 | 9 | AY.91 | 0.006574 |
S | 25 | P25L | cCc | cTc | 9 | 9 | B.1.177.86 | 0.001651 |
S | 25 | P25L | cCc | cTc | 8 | 8 | AY.47 | 0.000249 |
S | 25 | P25L | cCc | cTc | 7 | 7 | AY.111 | 0.001282 |
S | 25 | P25L | cCc | cTc | 7 | 7 | AY.39 | 0.000173 |
S | 25 | P25L | cCc | cTc | 7 | 7 | B.1.1.214 | 0.000388 |
S | 25 | P25L | cCc | cTc | 7 | 7 | B.1.429 | 0.000165 |
S | 25 | P25L | cCc | cTc | 6 | 6 | AY.14 | 0.000528 |
S | 25 | P25L | cCc | cTc | 6 | 6 | B.1.258 | 0.000399 |
S | 25 | P25L | cCc | cTc | 6 | 6 | B.1.369 | 0.001711 |
S | 25 | P25L | cCc | cTc | 6 | 6 | P.1.1 | 0.001906 |
S | 25 | P25L | cCc | cTc | 6 | 6 | P.1.14 | 0.000287 |
S | 25 | P25L | cCc | cTc | 5 | 5 | AY.117 | 0.000423 |
S | 25 | P25L | cCc | cTc | 5 | 5 | B.1.1.519 | 0.000199 |
S | 25 | P25L | cCc | cTc | 5 | 5 | P.1.13 | 0.004492 |
S | 25 | P25L | cCC | cTA | 2 | 4 | 0.111111 | |
S | 25 | P25L | cCC | cTT | 2 | 4 | 0.111111 | |
S | 25 | P25L | cCc | cTc | 4 | 4 | AY.110 | 0.000451 |
S | 25 | P25L | cCc | cTc | 4 | 4 | AY.37 | 0.001264 |
S | 25 | P25L | cCc | cTc | 4 | 4 | AY.39.1 | 0.000158 |
S | 25 | P25L | cCc | cTc | 4 | 4 | B.1.1.33 | 0.001684 |
S | 25 | P25L | cCc | cTc | 4 | 4 | B.1.526 | 0.000094 |
S | 25 | P25L | cCc | cTc | 3 | 3 | A | 0.001161 |
S | 25 | P25L | cCc | cTc | 3 | 3 | AY.36 | 0.000445 |
S | 25 | P25L | cCc | cTc | 3 | 3 | AY.5 | 0.000062 |
S | 25 | P25L | cCc | cTc | 3 | 3 | AY.59 | 0.001589 |
S | 25 | P25L | cCc | cTc | 3 | 3 | AY.99.2 | 0.000276 |
S | 25 | P25L | cCc | cTc | 3 | 3 | B.1.1.176 | 0.001318 |
S | 25 | P25L | cCC | cTT | 3 | 3 | B.1.1.37 | 0.000579 |
S | 25 | P25L | cCc | cTc | 3 | 3 | C.37 | 0.000348 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.100 | 0.000092 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.23 | 0.000139 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.33 | 0.000134 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.4.2 | 0.000043 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.46 | 0.000208 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.48 | 0.00093 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.6 | 0.000082 |
S | 25 | P25L | cCc | cTc | 2 | 2 | AY.9 | 0.000135 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.1.70 | 0.000682 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.1.71 | 0.012121 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.111 | 0.00235 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.177.17 | 0.001642 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.177.7 | 0.00033 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.234 | 0.000264 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.243 | 0.000139 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.311 | 0.000549 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.351.2 | 0.000605 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.525 | 0.000226 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.596 | 0.000174 |
S | 25 | P25L | cCc | cTc | 2 | 2 | B.1.637 | 0.000146 |
S | 25 | P25L | cCc | cTc | 2 | 2 | C.36.3 | 0.001134 |
S | 25 | P25L | cCc | cTc | 2 | 2 | P.1.12 | 0.000968 |
S | 25 | P25L | cCc | cTc | 2 | 2 | P.2 | 0.000373 |
S | 25 | P25L | cCc | cTc | 2 | 2 | U.3 | 0.007722 |
S | 25 | P25L | cCc | cTc | 1 | 1 | A.2.5 | 0.000499 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AD.2 | 0.000219 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AU.2 | 0.002421 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.101 | 0.00049 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.116.1 | 0.000311 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.119 | 0.000035 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.12 | 0.000316 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.120.1 | 0.000321 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.121 | 0.000135 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.13 | 0.000161 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.16.1 | 0.00047 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.23.1 | 0.000417 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.26 | 0.000028 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.27 | 0.000065 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.34 | 0.000097 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.38 | 0.000499 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.42 | 0.00004 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.46.2 | 0.000635 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.46.4 | 0.000165 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.46.5 | 0.000198 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.49 | 0.003195 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.5.2 | 0.002463 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.5.4 | 0.000277 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.7 | 0.000196 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.75 | 0.000056 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.8 | 0.000606 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.88 | 0.000884 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.9.2 | 0.000037 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.93 | 0.000273 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.98 | 0.000079 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.98.1 | 0.000048 |
S | 25 | P25L | cCc | cTc | 1 | 1 | AY.99 | 0.001049 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.1.1 | 0.000327 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.1.180 | 0.010753 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.1.261 | 0.008621 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.1.372 | 0.000689 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.1.391 | 0.008547 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.1.434 | 0.000349 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.127 | 0.002198 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.177.15 | 0.000631 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.177.58 | 0.001332 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.177.60 | 0.000218 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.221 | 0.000071 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.258.17 | 0.000104 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.265 | 0.001271 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.329 | 0.000608 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.36.1 | 0.00114 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.36.31 | 0.001751 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.396 | 0.000706 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.436 | 0.001029 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.438.1 | 0.000107 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.470 | 0.001404 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.561 | 0.000397 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.576 | 0.000907 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.617.1 | 0.000129 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.1.621 | 0.000089 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.23 | 0.002924 |
S | 25 | P25L | cCc | cTc | 1 | 1 | B.6 | 0.00091 |
S | 25 | P25L | cCc | cTc | 1 | 1 | C.1 | 0.002392 |
S | 25 | P25L | cCc | cTc | 1 | 1 | C.35 | 0.000774 |
S | 25 | P25L | cCc | cTc | 1 | 1 | D.2 | 0.000075 |
S | 25 | P25L | cCc | cTc | 1 | 1 | P.1.15 | 0.000232 |
S | 25 | P25L | cCc | cTc | 1 | 1 | P.1.7 | 0.000319 |
S | 25 | P25L | cCc | cTc | 1 | 1 | Q.1 | 0.000126 |
S | 25 | P25L | cCc | cTc | 1 | 1 | Q.4 | 0.000455 |
S | 25 | P25L | cCc | cTc | 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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