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 |
ORF3a | 104 | P104S | nonsyn | Cct | Tct | 32762 | 32757 | 0.999847 | 25702-25704 |
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 |
ORF3a | 104 | P104S | Cct | Tct | 32757 | 32762 | All | 0.006265 |
ORF3a | 104 | P104S | Cct | Tct | 24446 | 24446 | AY.103 | 0.151787 |
ORF3a | 104 | P104S | Cct | Tct | 2653 | 2653 | B.1.1.7 | 0.002375 |
ORF3a | 104 | P104S | Cct | Tct | 2265 | 2265 | AY.24 | 0.976293 |
ORF3a | 104 | P104S | Cct | Tct | 1392 | 1392 | B.1.617.2 | 0.005241 |
ORF3a | 104 | P104S | Cct | Tct | 528 | 528 | AY.4 | 0.000822 |
ORF3a | 104 | P104S | Cct | Tct | 156 | 156 | AY.108 | 0.171996 |
ORF3a | 104 | P104S | Cct | Tct | 141 | 141 | AY.6 | 0.005799 |
ORF3a | 104 | P104S | Cct | Tct | 89 | 89 | AY.43 | 0.000394 |
ORF3a | 104 | P104S | Cct | Tct | 87 | 87 | AY.25 | 0.000523 |
ORF3a | 104 | P104S | Cct | Tct | 85 | 85 | B.1.258 | 0.005656 |
ORF3a | 104 | P104S | Cct | Tct | 82 | 82 | B.1 | 0.000751 |
ORF3a | 104 | P104S | Cct | Tct | 74 | 74 | B.1.2 | 0.000652 |
ORF3a | 104 | P104S | Cct | Tct | 54 | 54 | AY.44 | 0.000329 |
ORF3a | 104 | P104S | Cct | Tct | 44 | 44 | B.1.160 | 0.001372 |
ORF3a | 104 | P104S | Cct | Tct | 34 | 34 | AY.33 | 0.00227 |
ORF3a | 104 | P104S | Cct | Tct | 33 | 33 | B.1.177 | 0.000435 |
ORF3a | 104 | P104S | Cct | Tct | 26 | 26 | AY.117 | 0.002197 |
ORF3a | 104 | P104S | Cct | Tct | 26 | 26 | C.37 | 0.003018 |
ORF3a | 104 | P104S | Cct | Tct | 26 | 26 | P.1 | 0.00041 |
ORF3a | 104 | P104S | Cct | Tct | 24 | 24 | AY.3 | 0.000239 |
ORF3a | 104 | P104S | Cct | Tct | 16 | 16 | B.1.1 | 0.00029 |
ORF3a | 104 | P104S | Cct | Tct | 15 | 15 | Q.8 | 0.002474 |
ORF3a | 104 | P104S | Cct | Tct | 13 | 13 | AY.20 | 0.000505 |
ORF3a | 104 | P104S | Cct | Tct | 12 | 12 | AY.62 | 0.005229 |
ORF3a | 104 | P104S | Cct | Tct | 11 | 11 | AY.26 | 0.000311 |
ORF3a | 104 | P104S | Cct | Tct | 11 | 11 | AY.5 | 0.000227 |
ORF3a | 104 | P104S | Cct | Tct | 11 | 11 | B.1.258.17 | 0.001144 |
ORF3a | 104 | P104S | Cct | Tct | 11 | 11 | B.1.596 | 0.000959 |
ORF3a | 104 | P104S | Cct | Tct | 10 | 10 | B.1.637 | 0.000731 |
ORF3a | 104 | P104S | Cct | Tct | 10 | 10 | Q.1 | 0.001263 |
ORF3a | 104 | P104S | Cct | Tct | 9 | 9 | AY.23 | 0.000628 |
ORF3a | 104 | P104S | Cct | Tct | 9 | 9 | AY.37 | 0.002845 |
ORF3a | 104 | P104S | Cct | Tct | 9 | 9 | B.1.264.1 | 0.428571 |
ORF3a | 104 | P104S | Cct | Tct | 9 | 9 | B.1.351 | 0.000268 |
ORF3a | 104 | P104S | Cct | Tct | 9 | 9 | B.1.427 | 0.000454 |
ORF3a | 104 | P104S | Cct | Tct | 8 | 8 | AY.118 | 0.000501 |
ORF3a | 104 | P104S | Cct | Tct | 8 | 8 | AY.9 | 0.000541 |
ORF3a | 104 | P104S | Cct | Tct | 8 | 8 | B.1.1.519 | 0.000318 |
ORF3a | 104 | P104S | Cct | Tct | 8 | 8 | B.1.237 | 0.039801 |
ORF3a | 104 | P104S | Cct | Tct | 8 | 8 | B.1.621 | 0.000708 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 7 | 0.222222 | |
ORF3a | 104 | P104S | Cct | Tct | 7 | 7 | AY.119 | 0.000247 |
ORF3a | 104 | P104S | Cct | Tct | 7 | 7 | AY.45 | 0.000852 |
ORF3a | 104 | P104S | Cct | Tct | 7 | 7 | B.1.1.25 | 0.00398 |
ORF3a | 104 | P104S | Cct | Tct | 7 | 7 | B.1.429 | 0.000165 |
ORF3a | 104 | P104S | Cct | Tct | 7 | 7 | B.1.526 | 0.000165 |
ORF3a | 104 | P104S | Cct | Tct | 6 | 6 | B.1.1.216 | 0.005343 |
ORF3a | 104 | P104S | Cct | Tct | 6 | 6 | B.1.36 | 0.000875 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | AY.4.2.1 | 0.000745 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | AY.60 | 0.00469 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | AY.70 | 0.001043 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | AY.98.1 | 0.000242 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | B | 0.000639 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | B.1.609 | 0.002397 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | P.1.12 | 0.00242 |
ORF3a | 104 | P104S | Cct | Tct | 5 | 5 | Q.3 | 0.000725 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | AY.116 | 0.001147 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | AY.13 | 0.000644 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | AY.39 | 0.000099 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | AY.4.2 | 0.000087 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | AY.42 | 0.000161 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | AY.46 | 0.000416 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | AY.47 | 0.000124 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | B.1.1.263 | 0.006231 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | B.1.177.40 | 0.020619 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | B.1.234 | 0.000528 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | B.1.525 | 0.000453 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 4 | B.1.91 | 0.004149 |
ORF3a | 104 | P104S | Cct | Tct | 4 | 4 | P.1.15 | 0.000929 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | AY.113 | 0.000427 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | AY.32 | 0.001597 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | AY.34 | 0.000291 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | AY.67 | 0.001393 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | AY.75 | 0.000168 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | AY.9.2 | 0.00011 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | AY.92 | 0.000862 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | B.1.1.189 | 0.004539 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | B.1.36.27 | 0.00229 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | B.1.575 | 0.00091 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | C.14 | 0.012987 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | P.1.1 | 0.000953 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | P.1.14 | 0.000143 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | P.1.2 | 0.003468 |
ORF3a | 104 | P104S | Cct | Tct | 3 | 3 | P.2 | 0.00056 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | AY.46.4 | 0.000329 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | AY.57 | 0.001312 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | AY.58 | 0.001815 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | AY.74 | 0.000231 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | AY.98 | 0.000158 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | AY.99.2 | 0.000184 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.1.214 | 0.000111 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.1.317 | 0.000823 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.1.39 | 0.001019 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.177.57 | 0.000562 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.177.83 | 0.002963 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.221 | 0.000142 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.369 | 0.00057 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.451 | 0.016393 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.1.621.1 | 0.001012 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | B.52 | 0.020202 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | C.35 | 0.001548 |
ORF3a | 104 | P104S | Cct | Tct | 2 | 2 | P.1.10 | 0.000539 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | A.12 | 0.166667 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | A.2.5.1 | 0.004808 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AD.2 | 0.000219 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AM.1 | 0.111111 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.100 | 0.000046 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.101 | 0.00049 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.116.1 | 0.000311 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.16 | 0.00038 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.29.1 | 0.000221 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.35 | 0.000233 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.39.1 | 0.00004 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.4.3 | 0.000842 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.46.6 | 0.000072 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.48 | 0.000465 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.5.3 | 0.000337 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.53 | 0.000288 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.54 | 0.000095 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.61 | 0.000105 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.63 | 0.000387 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.69 | 0.000187 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.75.1 | 0.00018 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.84 | 0.000437 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.86 | 0.00083 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.91 | 0.00073 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | AY.95 | 0.000761 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.171 | 0.003676 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.207 | 0.001182 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.222 | 0.000204 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.311 | 0.000358 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.312 | 0.001912 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.329 | 0.003846 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.344 | 0.010753 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.351 | 0.002793 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.385 | 0.004464 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.47 | 0.005348 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.1.515 | 0.02 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.115 | 0.021739 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.160.25 | 0.011111 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.177.41 | 0.0025 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.177.44 | 0.000519 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.177.75 | 0.001041 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.258.11 | 0.000396 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.258.12 | 0.007874 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.336 | 0.002439 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.367 | 0.000792 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.391 | 0.001127 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.399 | 0.001934 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.409 | 0.000781 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.422 | 0.000812 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.438.1 | 0.000107 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.466.2 | 0.000391 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.470 | 0.001404 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.499 | 0.00105 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.555 | 0.022222 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.565 | 0.00081 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.580 | 0.004065 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.582 | 0.000491 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.595 | 0.000261 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.617.1 | 0.000129 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.620 | 0.000946 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | B.1.631 | 0.003367 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | C.36.3 | 0.000567 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | C.39 | 0.018868 |
ORF3a | 104 | P104S | Cct | Tct | 1 | 1 | P.1.17 | 0.000162 |
ORF3a | 104 | P104S | Cct | Tct | 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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