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 | 16 | T16T | syn | acG | acT | 6743 | 4669 | 0.692422 | 28319-28321 |
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 | 16 | T16T | acG | acT | 4669 | 6743 | All | 0.000893 |
N | 16 | T16T | acG | acT | 1063 | 1130 | B.1.1.7 | 0.000952 |
N | 16 | T16T | acG | acT | 863 | 893 | AY.4 | 0.001343 |
N | 16 | T16T | acG | acT | 306 | 306 | B.1.234 | 0.040375 |
N | 16 | T16T | acG | acT | 103 | 176 | B.1.2 | 0.000907 |
N | 16 | T16T | acG | acT | 121 | 175 | B.1 | 0.001108 |
N | 16 | T16T | acG | acT | 138 | 146 | B.1.617.2 | 0.00052 |
N | 16 | T16T | acG | acT | 141 | 141 | B.1.177.12 | 0.02139 |
N | 16 | T16T | acG | acT | 82 | 119 | B.1.177 | 0.00108 |
N | 16 | T16T | acG | acT | 44 | 115 | B.1.1 | 0.000798 |
N | 16 | T16T | acG | acT | 113 | 114 | AY.74 | 0.013068 |
N | 16 | T16T | acG | acT | 25 | 105 | B.1.429 | 0.000588 |
N | 16 | T16T | acG | acT | 94 | 95 | B.1.1.50 | 0.063815 |
N | 16 | T16T | acG | acT | 94 | 94 | AY.42 | 0.003782 |
N | 16 | T16T | acG | acT | 77 | 87 | AY.103 | 0.000478 |
N | 16 | T16T | acG | acT | 82 | 82 | B.1.1.266 | 1 |
N | 16 | T16T | acG | acT | 67 | 77 | AY.43 | 0.000297 |
N | 16 | T16T | acG | acT | 58 | 67 | AY.3 | 0.000577 |
N | 16 | T16T | acG | acT | 65 | 65 | U.2 | 0.570175 |
N | 16 | T16T | acG | acT | 53 | 64 | P.1 | 0.000835 |
N | 16 | T16T | acG | acT | 60 | 60 | AY.4.5 | 0.00645 |
N | 16 | T16T | acG | acT | 51 | 60 | B.1.160 | 0.001591 |
N | 16 | T16T | acG | acT | 59 | 59 | AY.54 | 0.005625 |
N | 16 | T16T | acG | acT | 40 | 52 | AY.25 | 0.000241 |
N | 16 | T16T | acG | acT | 12 | 52 | B.1.1.519 | 0.000477 |
N | 16 | T16T | acG | acT | 46 | 51 | AY.44 | 0.00028 |
N | 16 | T16T | acG | acT | 49 | 49 | B.1.177.81 | 0.009277 |
N | 16 | T16T | acG | acT | 5 | 39 | B.1.1.1 | 0.001633 |
N | 16 | T16T | acG | acT | 30 | 32 | AY.46.6 | 0.002166 |
N | 16 | T16T | acG | acT | 31 | 31 | AY.102 | 0.000822 |
N | 16 | T16T | acG | acT | 4 | 31 | B.1.1.63 | 0.001543 |
N | 16 | T16T | acG | acT | 1 | 29 | B.1.466.2 | 0.000391 |
N | 16 | T16T | acG | acT | 28 | 28 | AY.45 | 0.003407 |
N | 16 | T16T | acG | acT | 22 | 27 | B.1.351 | 0.000654 |
N | 16 | T16T | acG | acT | 25 | 25 | B.1.1.47 | 0.13369 |
N | 16 | T16T | acG | acT | 25 | 25 | B.1.177.60 | 0.005461 |
N | 16 | T16T | acG | acT | 23 | 24 | B.1.243 | 0.0016 |
N | 16 | T16T | acG | acT | 20 | 21 | AY.39 | 0.000494 |
N | 16 | T16T | acG | acT | 21 | 21 | AY.98.1 | 0.001017 |
N | 16 | T16T | acG | acT | 7 | 21 | B.1.1.216 | 0.006233 |
N | 16 | T16T | acG | acT | 7 | 20 | B.1.258 | 0.000466 |
N | 16 | T16T | acG | acT | 19 | 20 | B.1.526 | 0.000447 |
N | 16 | T16T | acG | acT | 2 | 19 | B.1.1.305 | 0.007722 |
N | 16 | T16T | acG | acT | 18 | 18 | AY.119 | 0.000636 |
N | 16 | T16T | acG | acT | 13 | 16 | AY.121 | 0.001759 |
N | 16 | T16T | acG | acT | 15 | 15 | B.1.499 | 0.015756 |
N | 16 | T16T | acG | acT | 10 | 14 | AY.4.2 | 0.000217 |
N | 16 | T16T | acG | acT | 3 | 14 | AY.98 | 0.000237 |
N | 16 | T16T | acG | acT | 13 | 13 | AY.3.1 | 0.001108 |
N | 16 | T16T | acG | acT | 13 | 13 | B.1.36.17 | 0.006423 |
N | 16 | T16T | acG | acT | 3 | 13 | P.1.14 | 0.000143 |
N | 16 | T16T | acG | acT | 12 | 12 | AY.120 | 0.000446 |
N | 16 | T16T | acG | acT | 9 | 11 | AY.6 | 0.00037 |
N | 16 | T16T | acG | acT | 11 | 11 | B.1.617.1 | 0.001419 |
N | 16 | T16T | acG | acT | 10 | 10 | B.1.517 | 0.00427 |
N | 16 | T16T | acG | acT | 10 | 10 | B.1.523 | 0.02451 |
N | 16 | T16T | acG | acT | 8 | 9 | AY.118 | 0.000501 |
N | 16 | T16T | acG | acT | 8 | 9 | AY.29 | 0.000126 |
N | 16 | T16T | acG | acT | 8 | 9 | AY.75 | 0.000448 |
N | 16 | T16T | acG | acT | 8 | 9 | B.1.396 | 0.005646 |
N | 16 | T16T | acG | acT | 5 | 8 | AY.9.2 | 0.000184 |
N | 16 | T16T | acG | acT | 5 | 8 | B.1.36 | 0.00073 |
N | 16 | T16T | acG | acT | 7 | 7 | AY.26 | 0.000198 |
N | 16 | T16T | acG | acT | 7 | 7 | AY.36 | 0.001037 |
N | 16 | T16T | acG | acT | 7 | 7 | AY.41 | 0.002058 |
N | 16 | T16T | acG | acT | 6 | 7 | AY.48 | 0.002791 |
N | 16 | T16T | acG | acT | 6 | 7 | AY.61 | 0.000629 |
N | 16 | T16T | acG | acT | 5 | 6 | AY.20 | 0.000194 |
N | 16 | T16T | acG | acT | 6 | 6 | AY.5 | 0.000124 |
N | 16 | T16T | acG | acT | 6 | 6 | B.1.499.1 | 0.666667 |
N | 16 | T16T | acG | acT | 4 | 6 | P.1.15 | 0.000929 |
N | 16 | T16T | acG | acT | 5 | 5 | AY.100 | 0.00023 |
N | 16 | T16T | acG | acT | 5 | 5 | AY.4.2.1 | 0.000745 |
N | 16 | T16T | acG | acT | 1 | 5 | B.1.1.25 | 0.000569 |
N | 16 | T16T | acG | acT | 5 | 5 | B.1.258.14 | 0.004902 |
N | 16 | T16T | acG | acT | 3 | 5 | B.1.525 | 0.000339 |
N | 16 | T16T | acG | acT | 5 | 5 | B.1.619.1 | 0.003207 |
N | 16 | T16T | acG | acT | 3 | 5 | B.1.621 | 0.000266 |
N | 16 | T16T | acG | acT | 5 | 5 | P.2 | 0.000933 |
N | 16 | T16T | acG | acT | 4 | 4 | A.2 | 0.002647 |
N | 16 | T16T | acG | acT | 4 | 4 | AY.120.1 | 0.001284 |
N | 16 | T16T | acG | acT | 4 | 4 | AY.2 | 0.001425 |
N | 16 | T16T | acG | acT | 3 | 4 | AY.46 | 0.000312 |
N | 16 | T16T | acG | acT | 3 | 4 | AY.47 | 0.000093 |
N | 16 | T16T | acG | acT | 1 | 4 | AY.77 | 0.001127 |
N | 16 | T16T | acG | acT | 3 | 4 | B.1.1.448 | 0.006098 |
N | 16 | T16T | acG | acT | 4 | 4 | B.1.177.75 | 0.004162 |
N | 16 | T16T | acG | acT | 3 | 4 | B.1.36.29 | 0.001552 |
N | 16 | T16T | acG | acT | 2 | 4 | B.1.582 | 0.000981 |
N | 16 | T16T | acG | acT | 4 | 4 | B.1.596 | 0.000349 |
N | 16 | T16T | acG | acT | 4 | 4 | C.37 | 0.000464 |
N | 16 | T16T | acG | acT | 4 | 4 | Q.8 | 0.00066 |
N | 16 | T16T | acG | acT | 1 | 3 | A.23.1 | 0.000704 |
N | 16 | T16T | acG | acT | 1 | 3 | AY.111 | 0.000183 |
N | 16 | T16T | acG | acT | 3 | 3 | AY.117 | 0.000254 |
N | 16 | T16T | acG | acT | 2 | 3 | AY.34 | 0.000194 |
N | 16 | T16T | acG | acT | 3 | 3 | AY.46.3 | 0.002801 |
N | 16 | T16T | acG | acT | 3 | 3 | AY.46.4 | 0.000494 |
N | 16 | T16T | acG | acT | 1 | 3 | B.1.1.277 | 0.000759 |
N | 16 | T16T | acG | acT | 2 | 3 | B.1.1.317 | 0.000823 |
N | 16 | T16T | acG | acT | 3 | 3 | B.1.1.397 | 0.006757 |
N | 16 | T16T | acG | acT | 1 | 3 | B.1.177.73 | 0.000566 |
N | 16 | T16T | acG | acT | 1 | 3 | B.1.177.8 | 0.000752 |
N | 16 | T16T | acG | acT | 3 | 3 | B.1.239 | 0.003663 |
N | 16 | T16T | acG | acT | 2 | 3 | B.1.36.18 | 0.00084 |
N | 16 | T16T | acG | acT | 3 | 3 | B.1.427 | 0.000151 |
N | 16 | T16T | acG | acT | 3 | 3 | B.1.470 | 0.004213 |
N | 16 | T16T | acG | acT | 3 | 3 | B.1.575 | 0.00091 |
N | 16 | T16T | acG | acT | 2 | 3 | B.1.595 | 0.000522 |
N | 16 | T16T | acG | acT | 3 | 3 | C.18 | 0.007772 |
N | 16 | T16T | acG | acT | 3 | 3 | C.31 | 0.053571 |
N | 16 | T16T | acG | acT | 1 | 3 | C.36 | 0.000911 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.110 | 0.000225 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.113 | 0.000285 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.16.1 | 0.00094 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.23 | 0.000139 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.27 | 0.000129 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.33 | 0.000134 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.35 | 0.000466 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.37 | 0.000632 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.68 | 0.000547 |
N | 16 | T16T | acG | acT | 1 | 2 | AY.69 | 0.000187 |
N | 16 | T16T | acG | acT | 1 | 2 | AY.75.1 | 0.00018 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.84 | 0.000875 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.9.1 | 0.000167 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.93 | 0.000546 |
N | 16 | T16T | acG | acT | 2 | 2 | AY.99.2 | 0.000184 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.1.129 | 0.018349 |
N | 16 | T16T | acG | acT | 1 | 2 | B.1.1.141 | 0.002012 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.1.207 | 0.002364 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.1.267 | 0.020202 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.1.297 | 0.004474 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.160.16 | 0.001859 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.177.4 | 0.000422 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.177.7 | 0.00033 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.22 | 0.002635 |
N | 16 | T16T | acG | acT | 1 | 2 | B.1.258.17 | 0.000104 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.36.22 | 0.002415 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.36.7 | 0.008 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.367 | 0.001585 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.369 | 0.00057 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.561 | 0.000794 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.564 | 0.000852 |
N | 16 | T16T | acG | acT | 2 | 2 | B.1.88.1 | 0.009615 |
N | 16 | T16T | acG | acT | 2 | 2 | K.2 | 0.08 |
N | 16 | T16T | acG | acT | 1 | 2 | P.1.17 | 0.000162 |
N | 16 | T16T | acG | acT | 2 | 2 | P.1.2 | 0.002312 |
N | 16 | T16T | acG | acT | 1 | 2 | Q.3 | 0.000145 |
N | 16 | T16T | acG | acT | 1 | 1 | A.2.5 | 0.000499 |
N | 16 | T16T | acG | acT | 1 | 1 | A.27 | 0.001656 |
N | 16 | T16T | acG | acT | 1 | 1 | AU.2 | 0.002421 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.10 | 0.00053 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.101 | 0.00049 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.106 | 0.000335 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.116 | 0.000287 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.116.1 | 0.000311 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.31 | 0.018519 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.38 | 0.000499 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.4.4 | 0.000409 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.40 | 0.000964 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.46.1 | 0.001027 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.51 | 0.000909 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.52 | 0.000814 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.56 | 0.001605 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.62 | 0.000436 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.64 | 0.000595 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.7 | 0.000196 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.7.1 | 0.000113 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.72 | 0.001361 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.73 | 0.000665 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.78 | 0.001541 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.86 | 0.00083 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.9 | 0.000068 |
N | 16 | T16T | acG | acT | 1 | 1 | AY.91 | 0.00073 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.1.231 | 0.003096 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.1.285 | 0.006536 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.1.409 | 0.002833 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.1.483 | 0.038462 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.1.5 | 0.008333 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.1.518 | 0.006329 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.1.90 | 0.1 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.177.20 | 0.001517 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.177.33 | 0.001645 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.177.44 | 0.000519 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.177.45 | 0.000381 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.177.46 | 0.000918 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.177.57 | 0.000281 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.177.82 | 0.000477 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.206 | 0.000816 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.221 | 0.000071 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.232 | 0.000537 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.237 | 0.004975 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.332 | 0.003497 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.349 | 0.000715 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.351.2 | 0.000303 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.36.16 | 0.001425 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.36.24 | 0.006173 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.36.35 | 0.002604 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.395 | 0.007042 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.400 | 0.000429 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.402 | 0.009804 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.426 | 0.001009 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.443 | 0.004673 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.452 | 0.013699 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.467 | 0.04 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.560 | 0.00463 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.570 | 0.002941 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.571 | 0.009709 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.576 | 0.000907 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.577 | 0.000687 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.628 | 0.000352 |
N | 16 | T16T | acG | acT | 1 | 1 | B.1.637 | 0.000073 |
N | 16 | T16T | acG | acT | 1 | 1 | B.39 | 0.002331 |
N | 16 | T16T | acG | acT | 1 | 1 | B.4.5 | 0.011905 |
N | 16 | T16T | acG | acT | 1 | 1 | C.36.3 | 0.000567 |
N | 16 | T16T | acG | acT | 1 | 1 | P.1.1 | 0.000318 |
N | 16 | T16T | acG | acT | 1 | 1 | P.1.16 | 0.000374 |
N | 16 | T16T | acG | acT | 1 | 1 | P.1.7 | 0.000319 |
N | 16 | T16T | acG | acT | 1 | 1 | Q.1 | 0.000126 |
N | 16 | T16T | acG | acT | 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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