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 | 1100 | T1100T | syn | acA | acG | 771 | 735 | 0.953307 | 24860-24862 | |
S | 1100 | T1100T | syn | acA | acT | 771 | 29 | 0.0376135 | 24860-24862 | |
S | 1100 | T1100T | syn | acA | acC | 771 | 7 | 0.00907912 | 24860-24862 | |
S | 1100 | T1100I | nonsyn | aCa | aTa | 252 | 251 | 0.996032 | 24860-24862 | |
S | 1100 | T1100I | nonsyn | aCA | aTT | 252 | 1 | 0.00396825 | 24860-24862 | |
S | 1100 | T1100K | nonsyn | aCa | aAa | 71 | 71 | 1 | 24860-24862 | |
S | 1100 | T1100A | nonsyn | Aca | Gca | 33 | 33 | 1 | 24860-24862 | |
S | 1100 | T1100S | nonsyn | Aca | Tca | 20 | 20 | 1 | 24860-24862 | |
S | 1100 | T1100del | del | ACA | --- | 17 | 17 | 1 | 24860-24862 | |
S | 1100 | T1100P | nonsyn | Aca | Cca | 3 | 3 | 1 | 24860-24862 | |
S | 1100 | T1100R | nonsyn | aCa | aGa | 3 | 3 | 1 | 24860-24862 | |
S | 1100 | T1100L | nonsyn | ACa | TTa | 2 | 2 | 1 | 24860-24862 | |
S | 1100 | T1100V | nonsyn | ACa | GTa | 1 | 1 | 1 | 24860-24862 | |
S | 1100 | T1100N | nonsyn | aCA | aAC | 1 | 1 | 1 | 24860-24862 | |
S | 1100 | T1100del1 | del | Aca | -ca | 1 | 1 | 1 | 24860-24862 |
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 | 1100 | T1100T | acA | acG | 735 | 771 | All | 0.000141 |
S | 1100 | T1100T | acA | acT | 29 | 771 | All | 0.000006 |
S | 1100 | T1100T | acA | acC | 7 | 771 | All | 0.000001 |
S | 1100 | T1100T | acA | acG | 507 | 507 | B.1.8 | 1 |
S | 1100 | T1100I | aCa | aTa | 251 | 252 | All | 0.000048 |
S | 1100 | T1100I | aCA | aTT | 1 | 252 | All | 0 |
S | 1100 | T1100K | aCa | aAa | 71 | 71 | All | 0.000014 |
S | 1100 | T1100K | aCa | aAa | 64 | 64 | AY.3 | 0.000637 |
S | 1100 | T1100T | acA | acG | 61 | 62 | B.1.1 | 0.001107 |
S | 1100 | T1100T | acA | acT | 1 | 62 | B.1.1 | 0.000018 |
S | 1100 | T1100I | aCa | aTa | 49 | 49 | B.1.1.7 | 0.000044 |
S | 1100 | T1100T | acA | acG | 41 | 48 | B.1.1.7 | 0.000037 |
S | 1100 | T1100T | acA | acT | 6 | 48 | B.1.1.7 | 0.000005 |
S | 1100 | T1100T | acA | acC | 1 | 48 | B.1.1.7 | 0.000001 |
S | 1100 | T1100I | aCa | aTa | 41 | 41 | AY.103 | 0.000255 |
S | 1100 | T1100I | aCa | aTa | 37 | 37 | AY.44 | 0.000225 |
S | 1100 | T1100A | Aca | Gca | 33 | 33 | All | 0.000006 |
S | 1100 | T1100T | acA | acG | 28 | 28 | AY.43 | 0.000124 |
S | 1100 | T1100T | acA | acG | 19 | 24 | B.1 | 0.000174 |
S | 1100 | T1100T | acA | acT | 3 | 24 | B.1 | 0.000027 |
S | 1100 | T1100T | acA | acC | 2 | 24 | B.1 | 0.000018 |
S | 1100 | T1100S | Aca | Tca | 20 | 20 | All | 0.000004 |
S | 1100 | T1100I | aCa | aTa | 19 | 19 | AY.4 | 0.00003 |
S | 1100 | T1100I | aCa | aTa | 18 | 18 | B.1.617.2 | 0.000068 |
S | 1100 | T1100del | ACA | --- | 17 | 17 | All | 0.000003 |
S | 1100 | T1100T | acA | acG | 14 | 14 | AY.47 | 0.000435 |
S | 1100 | T1100I | aCa | aTa | 10 | 10 | AY.25 | 0.00006 |
S | 1100 | T1100T | acA | acG | 9 | 9 | AY.3.1 | 0.000767 |
S | 1100 | T1100I | aCa | aTa | 8 | 8 | AY.43 | 0.000035 |
S | 1100 | T1100I | aCa | aTa | 8 | 8 | B.1 | 0.000073 |
S | 1100 | T1100A | Aca | Gca | 8 | 8 | B.1.1.7 | 0.000007 |
S | 1100 | T1100I | aCa | aTa | 7 | 7 | AY.26 | 0.000198 |
S | 1100 | T1100T | acA | acG | 7 | 7 | B.1.396 | 0.00494 |
S | 1100 | T1100T | acA | acG | 4 | 6 | AY.103 | 0.000025 |
S | 1100 | T1100T | acA | acT | 1 | 6 | AY.103 | 0.000006 |
S | 1100 | T1100T | acA | acC | 1 | 6 | AY.103 | 0.000006 |
S | 1100 | T1100T | acA | acG | 6 | 6 | B.1.2 | 0.000053 |
S | 1100 | T1100T | acA | acT | 6 | 6 | B.1.572 | 0.15 |
S | 1100 | T1100S | Aca | Tca | 5 | 5 | AY.25 | 0.00003 |
S | 1100 | T1100T | acA | acG | 4 | 5 | AY.4 | 0.000006 |
S | 1100 | T1100T | acA | acT | 1 | 5 | AY.4 | 0.000002 |
S | 1100 | T1100I | aCa | aTa | 4 | 4 | P.1 | 0.000063 |
S | 1100 | T1100A | Aca | Gca | 3 | 3 | 0.166667 | |
S | 1100 | T1100R | aCa | aGa | 3 | 3 | All | 0.000001 |
S | 1100 | T1100P | Aca | Cca | 3 | 3 | All | 0.000001 |
S | 1100 | T1100T | acA | acT | 3 | 3 | AY.102 | 0.00008 |
S | 1100 | T1100I | aCa | aTa | 3 | 3 | AY.39 | 0.000074 |
S | 1100 | T1100S | Aca | Tca | 3 | 3 | AY.4 | 0.000005 |
S | 1100 | T1100A | Aca | Gca | 3 | 3 | AY.42 | 0.000121 |
S | 1100 | T1100del | ACA | --- | 3 | 3 | B.1.1.7 | 0.000003 |
S | 1100 | T1100I | aCa | aTa | 3 | 3 | B.1.243 | 0.000209 |
S | 1100 | T1100T | acA | acG | 3 | 3 | B.1.258.17 | 0.000312 |
S | 1100 | T1100T | acA | acT | 3 | 3 | B.1.351 | 0.000089 |
S | 1100 | T1100A | Aca | Gca | 3 | 3 | B.1.429 | 0.000071 |
S | 1100 | T1100S | Aca | Tca | 3 | 3 | B.1.526 | 0.000071 |
S | 1100 | T1100T | acA | acG | 2 | 2 | 0.111111 | |
S | 1100 | T1100L | ACa | TTa | 2 | 2 | All | 0 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | AY.102 | 0.000053 |
S | 1100 | T1100K | aCa | aAa | 2 | 2 | AY.119 | 0.000071 |
S | 1100 | T1100del | ACA | --- | 2 | 2 | AY.120 | 0.000074 |
S | 1100 | T1100T | acA | acG | 2 | 2 | AY.20 | 0.000078 |
S | 1100 | T1100T | acA | acT | 1 | 2 | AY.23 | 0.00007 |
S | 1100 | T1100T | acA | acG | 1 | 2 | AY.23 | 0.00007 |
S | 1100 | T1100A | Aca | Gca | 2 | 2 | AY.25 | 0.000012 |
S | 1100 | T1100T | acA | acT | 2 | 2 | AY.29 | 0.000032 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | AY.3 | 0.00002 |
S | 1100 | T1100A | Aca | Gca | 2 | 2 | AY.3 | 0.00002 |
S | 1100 | T1100A | Aca | Gca | 2 | 2 | AY.4 | 0.000003 |
S | 1100 | T1100del | ACA | --- | 2 | 2 | AY.4 | 0.000003 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | AY.4.5 | 0.000215 |
S | 1100 | T1100del | ACA | --- | 2 | 2 | AY.43 | 0.000009 |
S | 1100 | T1100T | acA | acG | 2 | 2 | AY.5 | 0.000041 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | AY.64 | 0.00119 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | AY.75 | 0.000112 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | AY.9.1 | 0.000167 |
S | 1100 | T1100A | Aca | Gca | 2 | 2 | B.1 | 0.000018 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | B.1.1 | 0.000036 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | B.1.1.161 | 0.007067 |
S | 1100 | T1100T | acA | acG | 2 | 2 | B.1.1.25 | 0.001137 |
S | 1100 | T1100S | Aca | Tca | 2 | 2 | B.1.1.7 | 0.000002 |
S | 1100 | T1100A | Aca | Gca | 2 | 2 | B.1.177 | 0.000026 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | B.1.177 | 0.000026 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | B.1.2 | 0.000018 |
S | 1100 | T1100T | acA | acC | 1 | 2 | B.1.258 | 0.000067 |
S | 1100 | T1100T | acA | acG | 1 | 2 | B.1.258 | 0.000067 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | B.1.36.29 | 0.001035 |
S | 1100 | T1100A | Aca | Gca | 2 | 2 | B.1.402 | 0.019608 |
S | 1100 | T1100T | acA | acG | 2 | 2 | B.1.564.1 | 0.003155 |
S | 1100 | T1100K | aCa | aAa | 2 | 2 | B.1.609 | 0.000959 |
S | 1100 | T1100T | acA | acG | 2 | 2 | C.36.3 | 0.001134 |
S | 1100 | T1100T | acA | acG | 2 | 2 | C.37 | 0.000232 |
S | 1100 | T1100I | aCa | aTa | 2 | 2 | Q.2 | 0.001227 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | 0.055556 | |
S | 1100 | T1100V | ACa | GTa | 1 | 1 | 0.055556 | |
S | 1100 | T1100L | ACa | TTa | 1 | 1 | 0.055556 | |
S | 1100 | T1100S | Aca | Tca | 1 | 1 | 0.055556 | |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | A.28 | 0.002646 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AH.3 | 0.003802 |
S | 1100 | T1100V | ACa | GTa | 1 | 1 | All | 0 |
S | 1100 | T1100N | aCA | aAC | 1 | 1 | All | 0 |
S | 1100 | T1100del1 | Aca | -ca | 1 | 1 | All | 0 |
S | 1100 | T1100A | Aca | Gca | 1 | 1 | AY.103 | 0.000006 |
S | 1100 | T1100P | Aca | Cca | 1 | 1 | AY.103 | 0.000006 |
S | 1100 | T1100R | aCa | aGa | 1 | 1 | AY.103 | 0.000006 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AY.113 | 0.000142 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | AY.118 | 0.000063 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AY.119 | 0.000035 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AY.120 | 0.000037 |
S | 1100 | T1100del1 | Aca | -ca | 1 | 1 | AY.13 | 0.000161 |
S | 1100 | T1100A | Aca | Gca | 1 | 1 | AY.23 | 0.00007 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AY.25 | 0.000006 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AY.26 | 0.000028 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AY.29 | 0.000016 |
S | 1100 | T1100S | Aca | Tca | 1 | 1 | AY.3 | 0.00001 |
S | 1100 | T1100T | acA | acT | 1 | 1 | AY.35 | 0.000233 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | AY.36 | 0.000148 |
S | 1100 | T1100S | Aca | Tca | 1 | 1 | AY.39.1 | 0.00004 |
S | 1100 | T1100P | Aca | Cca | 1 | 1 | AY.4 | 0.000002 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AY.41 | 0.000294 |
S | 1100 | T1100S | Aca | Tca | 1 | 1 | AY.44 | 0.000006 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AY.45 | 0.000122 |
S | 1100 | T1100A | Aca | Gca | 1 | 1 | AY.46 | 0.000104 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AY.46.1 | 0.001027 |
S | 1100 | T1100A | Aca | Gca | 1 | 1 | AY.47 | 0.000031 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AY.54 | 0.000095 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AY.6 | 0.000041 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AY.67 | 0.000464 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AY.7.1 | 0.000113 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | AY.75.1 | 0.00018 |
S | 1100 | T1100I | aCA | aTT | 1 | 1 | AY.79 | 0.001211 |
S | 1100 | T1100T | acA | acG | 1 | 1 | AZ.2 | 0.000821 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | B | 0.000128 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | B.1 | 0.000009 |
S | 1100 | T1100R | aCa | aGa | 1 | 1 | B.1 | 0.000009 |
S | 1100 | T1100K | aCa | aAa | 1 | 1 | B.1.1 | 0.000018 |
S | 1100 | T1100S | Aca | Tca | 1 | 1 | B.1.1.144 | 0.028571 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.1.214 | 0.000055 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | B.1.1.434 | 0.000349 |
S | 1100 | T1100R | aCa | aGa | 1 | 1 | B.1.1.7 | 0.000001 |
S | 1100 | T1100L | ACa | TTa | 1 | 1 | B.1.1.7 | 0.000001 |
S | 1100 | T1100N | aCA | aAC | 1 | 1 | B.1.1.7 | 0.000001 |
S | 1100 | T1100T | acA | acC | 1 | 1 | B.1.1.70 | 0.000341 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | B.1.160 | 0.000031 |
S | 1100 | T1100S | Aca | Tca | 1 | 1 | B.1.177.57 | 0.000281 |
S | 1100 | T1100K | aCa | aAa | 1 | 1 | B.1.177.75 | 0.001041 |
S | 1100 | T1100K | aCa | aAa | 1 | 1 | B.1.2 | 0.000009 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.222 | 0.001692 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | B.1.351 | 0.00003 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.36.17 | 0.000494 |
S | 1100 | T1100S | Aca | Tca | 1 | 1 | B.1.36.18 | 0.00042 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.36.18 | 0.00042 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.367 | 0.000792 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | B.1.399 | 0.001934 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.427 | 0.00005 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.525 | 0.000113 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | B.1.595 | 0.000261 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | B.1.609 | 0.000479 |
S | 1100 | T1100T | acA | acG | 1 | 1 | B.1.617.1 | 0.000129 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | B.1.617.2 | 0.000004 |
S | 1100 | T1100P | Aca | Cca | 1 | 1 | B.1.617.2 | 0.000004 |
S | 1100 | T1100T | acA | acC | 1 | 1 | B.1.625 | 0.002353 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | B.1.630 | 0.005236 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | C.37 | 0.000116 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | D.2 | 0.000075 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | N.7 | 0.029412 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | P.1 | 0.000016 |
S | 1100 | T1100I | aCa | aTa | 1 | 1 | P.1.14 | 0.000048 |
S | 1100 | T1100del | ACA | --- | 1 | 1 | P.1.15 | 0.000232 |
S | 1100 | T1100T | acA | acT | 1 | 1 | P.1.7 | 0.000319 |
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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