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 |
ORF1ab/nsp1 | 5 | V5V | V5V | syn | gtC | gtT | 1811 | 1715 | 0.946991 | 278-280 |
ORF1ab/nsp1 | 5 | V5V | V5V | syn | gtC | gtA | 1811 | 95 | 0.0524572 | 278-280 |
ORF1ab/nsp1 | 5 | V5V | V5V | syn | gtC | gtG | 1811 | 1 | 0.000552181 | 278-280 |
Details of the mutation V5V 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 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1715 | 1811 | All | 0.000328 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 95 | 1811 | All | 0.000018 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtG | 1 | 1811 | All | 0 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 226 | 239 | B.1.1.7 | 0.000202 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 13 | 239 | B.1.1.7 | 0.000012 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 228 | 232 | AY.43 | 0.00101 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 3 | 232 | AY.43 | 0.000013 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtG | 1 | 232 | AY.43 | 0.000004 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 142 | 159 | B.1.617.2 | 0.000535 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 17 | 159 | B.1.617.2 | 0.000064 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 127 | 127 | AY.44 | 0.000773 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 91 | 91 | AY.41 | 0.026749 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 86 | 86 | B.1.243 | 0.005984 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 80 | 80 | A.28 | 0.21164 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 64 | 65 | B.1.2 | 0.000564 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 65 | B.1.2 | 0.000009 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 58 | 59 | AY.4 | 0.00009 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 59 | AY.4 | 0.000002 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 35 | 45 | AY.25 | 0.000211 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 10 | 45 | AY.25 | 0.00006 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 36 | 36 | AY.47 | 0.00112 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 28 | 33 | AY.39 | 0.000692 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 5 | 33 | AY.39 | 0.000124 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 30 | 31 | AY.3 | 0.000298 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 31 | AY.3 | 0.00001 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 30 | 30 | AY.33 | 0.002003 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 25 | 27 | B.1 | 0.000229 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 2 | 27 | B.1 | 0.000018 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 14 | 24 | B.1.177 | 0.000184 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 10 | 24 | B.1.177 | 0.000132 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 20 | 20 | AY.7 | 0.00392 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 14 | 19 | AY.102 | 0.000371 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 5 | 19 | AY.102 | 0.000133 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 17 | 18 | AY.103 | 0.000106 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 18 | AY.103 | 0.000006 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 16 | 16 | B.1.160 | 0.000499 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 13 | 13 | B.1.177.34 | 0.684211 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 13 | 13 | B.1.232 | 0.006985 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 13 | 13 | C.37 | 0.001509 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 12 | 12 | AY.121 | 0.001624 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 11 | 11 | B.1.1 | 0.0002 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 11 | 11 | B.1.351 | 0.000327 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 11 | 11 | B.1.429 | 0.000259 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 11 | 11 | B.1.596 | 0.000959 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 10 | 10 | AY.100 | 0.00046 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 9 | 9 | AY.20 | 0.00035 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 9 | 9 | B.1.36.31 | 0.015762 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 9 | 9 | P.1 | 0.000142 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 8 | 8 | AY.29 | 0.000126 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 8 | 8 | B.1.258 | 0.000532 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 7 | 7 | B.1.1.70 | 0.002387 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 7 | 7 | B.1.177.9 | 0.009321 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 6 | 6 | B.1.258.14 | 0.005882 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 6 | 6 | B.1.427 | 0.000303 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 5 | 5 | AY.61 | 0.000524 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 5 | 5 | AY.69 | 0.000933 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 5 | 5 | B.1.1.316 | 0.004625 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 5 | 5 | B.1.1.362 | 0.02809 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 5 | 5 | B.1.1.519 | 0.000199 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 5 | 5 | B.1.3 | 0.013089 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 4 | 4 | AY.36 | 0.000593 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 4 | 4 | AY.4.2 | 0.000087 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 2 | 4 | AY.46 | 0.000208 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 4 | AY.46 | 0.000208 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 4 | 4 | AY.98 | 0.000316 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 4 | 4 | B.1.1.214 | 0.000222 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 4 | 4 | B.1.36.29 | 0.002069 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | AY.118 | 0.000188 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 3 | AY.14 | 0.000176 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 3 | AY.14 | 0.000088 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | AY.26 | 0.000085 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | AY.5 | 0.000062 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | AY.59 | 0.001589 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | AY.64 | 0.001786 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | AY.9.2 | 0.00011 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | B.1.110.3 | 0.002155 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | B.1.161 | 0.051724 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | B.1.466.2 | 0.001174 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | B.1.577 | 0.002062 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 3 | 3 | B.1.582 | 0.001472 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.16 | 0.000759 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.27 | 0.000129 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.29.1 | 0.000441 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.3.1 | 0.000171 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 2 | 2 | AY.46.5 | 0.000397 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.56 | 0.00321 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 2 | AY.6 | 0.000041 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 2 | AY.6 | 0.000041 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 2 | AY.75 | 0.000056 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 2 | AY.75 | 0.000056 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.75.1 | 0.000361 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.90 | 0.001369 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | AY.92 | 0.000575 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.1.220 | 0.003717 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.1.222 | 0.000408 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.1.348 | 0.001592 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.1.398 | 0.006452 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.1.512 | 0.057143 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.177.73 | 0.001133 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.311 | 0.000549 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.378 | 0.013699 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.526 | 0.000047 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.1.595 | 0.000522 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | B.55 | 0.0059 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | D.2 | 0.00015 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 2 | P.2 | 0.000187 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 2 | P.2 | 0.000187 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 2 | 2 | Q.8 | 0.00033 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | A | 0.000387 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | A.2 | 0.000662 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | A.2.5.1 | 0.004808 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AD.2 | 0.000219 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.107 | 0.000466 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 1 | AY.5.4 | 0.000277 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.62 | 0.000436 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.7.2 | 0.000559 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | AY.91 | 0.00073 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtA | 1 | 1 | AY.98.1 | 0.000048 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B | 0.000128 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.1.117 | 0.009709 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.1.134 | 0.011364 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.1.148 | 0.008772 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.1.284 | 0.000107 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.1.375 | 0.011905 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.1.434 | 0.000349 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.177.86 | 0.000183 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.214.2 | 0.0006 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.258.17 | 0.000104 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.277 | 0.02381 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.346 | 0.001311 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.351.2 | 0.000303 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.351.3 | 0.000876 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.391 | 0.001127 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.439 | 0.005917 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.459 | 0.004082 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.469 | 0.00361 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.550 | 0.013699 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.575 | 0.000303 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.627 | 0.00202 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | C.1.2 | 0.004255 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | C.37.1 | 0.002618 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | P.1.13 | 0.000898 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | Q.2 | 0.000613 |
ORF1ab/nsp1 | 5 | V5V | gtC | gtT | 1 | 1 | Q.4 | 0.000455 |
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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