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 |
ORF7a | 49 | L49L | syn | Cta | Tta | 3310 | 2969 | 0.896979 | 27538-27540 | |
ORF7a | 49 | L49L | syn | ctA | ctG | 3310 | 250 | 0.0755287 | 27538-27540 | |
ORF7a | 49 | L49L | syn | ctA | ctT | 3310 | 66 | 0.0199396 | 27538-27540 | |
ORF7a | 49 | L49L | syn | CtA | TtG | 3310 | 15 | 0.00453172 | 27538-27540 | |
ORF7a | 49 | L49L | syn | ctA | ctC | 3310 | 10 | 0.00302115 | 27538-27540 |
Details of the mutation L49L 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 |
ORF7a | 49 | L49L | Cta | Tta | 2969 | 3310 | All | 0.000568 |
ORF7a | 49 | L49L | ctA | ctG | 250 | 3310 | All | 0.000048 |
ORF7a | 49 | L49L | ctA | ctT | 66 | 3310 | All | 0.000013 |
ORF7a | 49 | L49L | CtA | TtG | 15 | 3310 | All | 0.000003 |
ORF7a | 49 | L49L | ctA | ctC | 10 | 3310 | All | 0.000002 |
ORF7a | 49 | L49L | Cta | Tta | 625 | 636 | AY.4 | 0.000973 |
ORF7a | 49 | L49L | ctA | ctG | 10 | 636 | AY.4 | 0.000016 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 636 | AY.4 | 0.000002 |
ORF7a | 49 | L49L | Cta | Tta | 390 | 390 | B.1.1.121 | 0.946602 |
ORF7a | 49 | L49L | Cta | Tta | 347 | 373 | B.1.617.2 | 0.001307 |
ORF7a | 49 | L49L | ctA | ctG | 22 | 373 | B.1.617.2 | 0.000083 |
ORF7a | 49 | L49L | ctA | ctT | 2 | 373 | B.1.617.2 | 0.000008 |
ORF7a | 49 | L49L | CtA | TtG | 2 | 373 | B.1.617.2 | 0.000008 |
ORF7a | 49 | L49L | Cta | Tta | 289 | 289 | AY.26 | 0.008182 |
ORF7a | 49 | L49L | Cta | Tta | 113 | 215 | B.1.1.7 | 0.000101 |
ORF7a | 49 | L49L | ctA | ctG | 96 | 215 | B.1.1.7 | 0.000086 |
ORF7a | 49 | L49L | ctA | ctC | 4 | 215 | B.1.1.7 | 0.000004 |
ORF7a | 49 | L49L | ctA | ctT | 2 | 215 | B.1.1.7 | 0.000002 |
ORF7a | 49 | L49L | Cta | Tta | 189 | 192 | AY.103 | 0.001174 |
ORF7a | 49 | L49L | ctA | ctT | 3 | 192 | AY.103 | 0.000019 |
ORF7a | 49 | L49L | Cta | Tta | 152 | 155 | AY.44 | 0.000925 |
ORF7a | 49 | L49L | ctA | ctT | 2 | 155 | AY.44 | 0.000012 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 155 | AY.44 | 0.000006 |
ORF7a | 49 | L49L | Cta | Tta | 137 | 137 | AY.75.1 | 0.024702 |
ORF7a | 49 | L49L | Cta | Tta | 74 | 83 | AY.25 | 0.000445 |
ORF7a | 49 | L49L | ctA | ctT | 5 | 83 | AY.25 | 0.00003 |
ORF7a | 49 | L49L | ctA | ctC | 2 | 83 | AY.25 | 0.000012 |
ORF7a | 49 | L49L | CtA | TtG | 2 | 83 | AY.25 | 0.000012 |
ORF7a | 49 | L49L | Cta | Tta | 70 | 72 | AY.43 | 0.00031 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 72 | AY.43 | 0.000009 |
ORF7a | 49 | L49L | Cta | Tta | 59 | 59 | AY.111 | 0.010806 |
ORF7a | 49 | L49L | Cta | Tta | 35 | 45 | B.1.2 | 0.000308 |
ORF7a | 49 | L49L | ctA | ctG | 9 | 45 | B.1.2 | 0.000079 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 45 | B.1.2 | 0.000009 |
ORF7a | 49 | L49L | Cta | Tta | 42 | 43 | AY.3 | 0.000418 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 43 | AY.3 | 0.00001 |
ORF7a | 49 | L49L | ctA | ctG | 20 | 31 | B.1.1.519 | 0.000794 |
ORF7a | 49 | L49L | Cta | Tta | 11 | 31 | B.1.1.519 | 0.000437 |
ORF7a | 49 | L49L | Cta | Tta | 26 | 29 | AY.102 | 0.000689 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 29 | AY.102 | 0.000027 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 29 | AY.102 | 0.000027 |
ORF7a | 49 | L49L | ctA | ctC | 1 | 29 | AY.102 | 0.000027 |
ORF7a | 49 | L49L | Cta | Tta | 27 | 27 | B.1.1.176 | 0.011863 |
ORF7a | 49 | L49L | ctA | ctT | 24 | 24 | B.1.177.4 | 0.005065 |
ORF7a | 49 | L49L | Cta | Tta | 21 | 21 | AY.9.2 | 0.000771 |
ORF7a | 49 | L49L | Cta | Tta | 11 | 16 | B.1 | 0.000101 |
ORF7a | 49 | L49L | ctA | ctG | 4 | 16 | B.1 | 0.000037 |
ORF7a | 49 | L49L | CtA | TtG | 1 | 16 | B.1 | 0.000009 |
ORF7a | 49 | L49L | CtA | TtG | 10 | 16 | B.1.177.21 | 0.000765 |
ORF7a | 49 | L49L | ctA | ctT | 6 | 16 | B.1.177.21 | 0.000459 |
ORF7a | 49 | L49L | Cta | Tta | 15 | 15 | AY.61 | 0.001572 |
ORF7a | 49 | L49L | Cta | Tta | 9 | 15 | B.1.1 | 0.000163 |
ORF7a | 49 | L49L | ctA | ctG | 6 | 15 | B.1.1 | 0.000109 |
ORF7a | 49 | L49L | ctA | ctG | 12 | 15 | D.2 | 0.0009 |
ORF7a | 49 | L49L | Cta | Tta | 3 | 15 | D.2 | 0.000225 |
ORF7a | 49 | L49L | Cta | Tta | 14 | 14 | AY.118 | 0.000877 |
ORF7a | 49 | L49L | ctA | ctG | 10 | 14 | AY.5 | 0.000206 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 14 | AY.5 | 0.000083 |
ORF7a | 49 | L49L | Cta | Tta | 13 | 13 | AY.23 | 0.000907 |
ORF7a | 49 | L49L | Cta | Tta | 12 | 12 | AY.68 | 0.003285 |
ORF7a | 49 | L49L | Cta | Tta | 11 | 11 | AY.16 | 0.004176 |
ORF7a | 49 | L49L | Cta | Tta | 11 | 11 | AY.4.2 | 0.000239 |
ORF7a | 49 | L49L | Cta | Tta | 11 | 11 | B.1.1.37 | 0.002122 |
ORF7a | 49 | L49L | Cta | Tta | 8 | 10 | AY.47 | 0.000249 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 10 | AY.47 | 0.000062 |
ORF7a | 49 | L49L | Cta | Tta | 10 | 10 | C.16 | 0.010604 |
ORF7a | 49 | L49L | ctA | ctG | 6 | 10 | P.1 | 0.000095 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 10 | P.1 | 0.000063 |
ORF7a | 49 | L49L | Cta | Tta | 9 | 9 | AY.57 | 0.005906 |
ORF7a | 49 | L49L | Cta | Tta | 8 | 9 | B.1.177 | 0.000105 |
ORF7a | 49 | L49L | ctA | ctC | 1 | 9 | B.1.177 | 0.000013 |
ORF7a | 49 | L49L | Cta | Tta | 8 | 8 | AY.29 | 0.000126 |
ORF7a | 49 | L49L | Cta | Tta | 7 | 7 | AY.110 | 0.000789 |
ORF7a | 49 | L49L | Cta | Tta | 7 | 7 | AY.119 | 0.000247 |
ORF7a | 49 | L49L | Cta | Tta | 6 | 7 | AY.33 | 0.000401 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 7 | AY.33 | 0.000067 |
ORF7a | 49 | L49L | ctA | ctT | 7 | 7 | B.1.1.39 | 0.003568 |
ORF7a | 49 | L49L | Cta | Tta | 7 | 7 | B.1.617.1 | 0.000903 |
ORF7a | 49 | L49L | Cta | Tta | 6 | 6 | AY.39 | 0.000148 |
ORF7a | 49 | L49L | Cta | Tta | 6 | 6 | AY.71 | 0.00285 |
ORF7a | 49 | L49L | Cta | Tta | 6 | 6 | B.1.177.81 | 0.001136 |
ORF7a | 49 | L49L | Cta | Tta | 6 | 6 | B.1.526 | 0.000141 |
ORF7a | 49 | L49L | ctA | ctG | 6 | 6 | Q.1 | 0.000758 |
ORF7a | 49 | L49L | Cta | Tta | 5 | 5 | AY.27 | 0.000324 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 5 | AY.36 | 0.000593 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 5 | AY.36 | 0.000148 |
ORF7a | 49 | L49L | Cta | Tta | 5 | 5 | AY.7 | 0.00098 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 5 | AY.75 | 0.000112 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 5 | AY.75 | 0.000112 |
ORF7a | 49 | L49L | ctA | ctC | 1 | 5 | AY.75 | 0.000056 |
ORF7a | 49 | L49L | Cta | Tta | 5 | 5 | B.1.466.2 | 0.001956 |
ORF7a | 49 | L49L | ctA | ctG | 5 | 5 | P.2 | 0.000933 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 4 | 0.111111 | |
ORF7a | 49 | L49L | ctA | ctT | 2 | 4 | 0.111111 | |
ORF7a | 49 | L49L | ctA | ctT | 3 | 4 | AY.116 | 0.00086 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 4 | AY.116 | 0.000287 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 4 | AY.120 | 0.000149 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 4 | AY.14 | 0.000352 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 4 | AY.46.6 | 0.000289 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 4 | AY.6 | 0.000165 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 4 | AY.84 | 0.00175 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 4 | B.1.160 | 0.000125 |
ORF7a | 49 | L49L | Cta | Tta | 4 | 4 | B.1.234 | 0.000528 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 4 | B.1.351 | 0.000059 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 4 | B.1.351 | 0.00003 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 4 | B.1.351 | 0.00003 |
ORF7a | 49 | L49L | Cta | Tta | 3 | 4 | B.1.429 | 0.000071 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 4 | B.1.429 | 0.000024 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 3 | AY.100 | 0.000092 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 3 | AY.100 | 0.000046 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 3 | AY.117 | 0.000169 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 3 | AY.117 | 0.000085 |
ORF7a | 49 | L49L | ctA | ctG | 3 | 3 | AY.13 | 0.000483 |
ORF7a | 49 | L49L | Cta | Tta | 3 | 3 | AY.3.1 | 0.000256 |
ORF7a | 49 | L49L | ctA | ctG | 3 | 3 | AY.39.1 | 0.000119 |
ORF7a | 49 | L49L | Cta | Tta | 3 | 3 | AY.42 | 0.000121 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 3 | AY.45 | 0.000122 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 3 | AY.45 | 0.000122 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 3 | AY.45 | 0.000122 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 3 | AY.46 | 0.000208 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 3 | AY.46 | 0.000104 |
ORF7a | 49 | L49L | Cta | Tta | 3 | 3 | AY.62 | 0.001307 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 3 | B.1.1.216 | 0.00089 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 3 | B.1.1.216 | 0.00089 |
ORF7a | 49 | L49L | ctA | ctC | 1 | 3 | B.1.1.216 | 0.00089 |
ORF7a | 49 | L49L | Cta | Tta | 3 | 3 | B.1.620 | 0.002838 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 3 | P.1.14 | 0.000096 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 3 | P.1.14 | 0.000048 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.106 | 0.00067 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.107 | 0.000932 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 2 | AY.19 | 0.002281 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.20 | 0.000078 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.30 | 0.000791 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.4.5 | 0.000215 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.46.2 | 0.001271 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.53 | 0.000575 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.7.1 | 0.000225 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.70 | 0.000417 |
ORF7a | 49 | L49L | ctA | ctT | 2 | 2 | AY.77 | 0.002255 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.98.1 | 0.000097 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | AY.99.2 | 0.000184 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 2 | B.1.1.28 | 0.000311 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 2 | B.1.1.28 | 0.000311 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 2 | B.1.1.33 | 0.000421 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 2 | B.1.1.33 | 0.000421 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | B.1.1.413 | 0.013793 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | B.1.1.70 | 0.000682 |
ORF7a | 49 | L49L | ctA | ctG | 2 | 2 | B.1.160.25 | 0.022222 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 2 | B.1.36 | 0.000146 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 2 | B.1.36 | 0.000146 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | B.1.596 | 0.000174 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 2 | B.1.637 | 0.000073 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 2 | B.1.637 | 0.000073 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | P.1.15 | 0.000465 |
ORF7a | 49 | L49L | Cta | Tta | 2 | 2 | P.1.4 | 0.001953 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | A.1 | 0.000282 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 1 | A.3 | 0.002096 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AD.2 | 0.000219 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.105 | 0.000643 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.109 | 0.00074 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.113 | 0.000142 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.120.2 | 0.001285 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.121 | 0.000135 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.2 | 0.000356 |
ORF7a | 49 | L49L | ctA | ctT | 1 | 1 | AY.29.1 | 0.000221 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | AY.32 | 0.000532 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.37 | 0.000316 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.46.3 | 0.000934 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.54 | 0.000095 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.67 | 0.000464 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.74 | 0.000116 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | AY.78 | 0.001541 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.90 | 0.000684 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.92 | 0.000287 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.93 | 0.000273 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | AY.98 | 0.000079 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.1 | 0.000327 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.117 | 0.009709 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.174 | 0.003378 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.192 | 0.002309 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.222 | 0.000204 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.311 | 0.000358 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.318 | 0.000302 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | B.1.1.348 | 0.000796 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | B.1.1.50 | 0.000679 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.1.89 | 0.006061 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.177.86 | 0.000183 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | B.1.222 | 0.001692 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.241 | 0.000812 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.258.9 | 0.005 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.298 | 0.002114 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | B.1.36.29 | 0.000517 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.389 | 0.001002 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.416.1 | 0.001563 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.499 | 0.00105 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | B.1.525 | 0.000113 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.575.1 | 0.002439 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | B.1.621 | 0.000089 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | C.36 | 0.000911 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | P.1.11 | 0.010204 |
ORF7a | 49 | L49L | ctA | ctG | 1 | 1 | P.1.16 | 0.000374 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | P.1.17 | 0.000162 |
ORF7a | 49 | L49L | Cta | Tta | 1 | 1 | Q.8 | 0.000165 |
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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