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 | 816 | S816S | syn | tcA | tcG | 1177 | 989 | 0.840272 | 24008-24010 | |
S | 816 | S816S | syn | tcA | tcT | 1177 | 142 | 0.120646 | 24008-24010 | |
S | 816 | S816S | syn | tcA | tcC | 1177 | 46 | 0.0390824 | 24008-24010 |
Details of the mutation S816S 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 | 816 | S816S | tcA | tcG | 989 | 1177 | All | 0.000189 |
S | 816 | S816S | tcA | tcT | 142 | 1177 | All | 0.000027 |
S | 816 | S816S | tcA | tcC | 46 | 1177 | All | 0.000009 |
S | 816 | S816S | tcA | tcG | 219 | 230 | B.1.1.7 | 0.000196 |
S | 816 | S816S | tcA | tcT | 9 | 230 | B.1.1.7 | 0.000008 |
S | 816 | S816S | tcA | tcC | 2 | 230 | B.1.1.7 | 0.000002 |
S | 816 | S816S | tcA | tcG | 191 | 191 | B.1.612 | 0.506631 |
S | 816 | S816S | tcA | tcG | 156 | 171 | AY.4 | 0.000243 |
S | 816 | S816S | tcA | tcT | 15 | 171 | AY.4 | 0.000023 |
S | 816 | S816S | tcA | tcG | 45 | 49 | B.1.617.2 | 0.000169 |
S | 816 | S816S | tcA | tcT | 3 | 49 | B.1.617.2 | 0.000011 |
S | 816 | S816S | tcA | tcC | 1 | 49 | B.1.617.2 | 0.000004 |
S | 816 | S816S | tcA | tcG | 39 | 40 | AY.44 | 0.000237 |
S | 816 | S816S | tcA | tcT | 1 | 40 | AY.44 | 0.000006 |
S | 816 | S816S | tcA | tcT | 28 | 39 | AY.43 | 0.000124 |
S | 816 | S816S | tcA | tcG | 11 | 39 | AY.43 | 0.000049 |
S | 816 | S816S | tcA | tcG | 36 | 38 | AY.33 | 0.002404 |
S | 816 | S816S | tcA | tcT | 2 | 38 | AY.33 | 0.000134 |
S | 816 | S816S | tcA | tcG | 35 | 35 | AY.5.3 | 0.011808 |
S | 816 | S816S | tcA | tcC | 33 | 33 | B.1.1.176 | 0.014499 |
S | 816 | S816S | tcA | tcG | 15 | 24 | AY.25 | 0.00009 |
S | 816 | S816S | tcA | tcT | 7 | 24 | AY.25 | 0.000042 |
S | 816 | S816S | tcA | tcC | 2 | 24 | AY.25 | 0.000012 |
S | 816 | S816S | tcA | tcG | 21 | 23 | P.1 | 0.000331 |
S | 816 | S816S | tcA | tcT | 2 | 23 | P.1 | 0.000032 |
S | 816 | S816S | tcA | tcG | 21 | 21 | AY.114 | 0.004853 |
S | 816 | S816S | tcA | tcG | 17 | 18 | AY.102 | 0.000451 |
S | 816 | S816S | tcA | tcT | 1 | 18 | AY.102 | 0.000027 |
S | 816 | S816S | tcA | tcG | 13 | 16 | B.1.221 | 0.000923 |
S | 816 | S816S | tcA | tcT | 3 | 16 | B.1.221 | 0.000213 |
S | 816 | S816S | tcA | tcT | 12 | 12 | B.1.429 | 0.000282 |
S | 816 | S816S | tcA | tcG | 8 | 11 | B.1.1 | 0.000145 |
S | 816 | S816S | tcA | tcT | 3 | 11 | B.1.1 | 0.000054 |
S | 816 | S816S | tcA | tcT | 8 | 9 | AY.13 | 0.001288 |
S | 816 | S816S | tcA | tcG | 1 | 9 | AY.13 | 0.000161 |
S | 816 | S816S | tcA | tcG | 5 | 9 | AY.29 | 0.000079 |
S | 816 | S816S | tcA | tcT | 4 | 9 | AY.29 | 0.000063 |
S | 816 | S816S | tcA | tcG | 9 | 9 | B.1.396 | 0.006351 |
S | 816 | S816S | tcA | tcT | 6 | 8 | AY.4.2 | 0.00013 |
S | 816 | S816S | tcA | tcC | 1 | 8 | AY.4.2 | 0.000022 |
S | 816 | S816S | tcA | tcG | 1 | 8 | AY.4.2 | 0.000022 |
S | 816 | S816S | tcA | tcG | 8 | 8 | AY.99 | 0.008395 |
S | 816 | S816S | tcA | tcG | 8 | 8 | B.1.258.17 | 0.000832 |
S | 816 | S816S | tcA | tcG | 5 | 7 | B.1.177 | 0.000066 |
S | 816 | S816S | tcA | tcC | 2 | 7 | B.1.177 | 0.000026 |
S | 816 | S816S | tcA | tcT | 4 | 6 | AY.103 | 0.000025 |
S | 816 | S816S | tcA | tcG | 1 | 6 | AY.103 | 0.000006 |
S | 816 | S816S | tcA | tcC | 1 | 6 | AY.103 | 0.000006 |
S | 816 | S816S | tcA | tcG | 6 | 6 | AY.20 | 0.000233 |
S | 816 | S816S | tcA | tcT | 3 | 6 | AY.3 | 0.00003 |
S | 816 | S816S | tcA | tcG | 3 | 6 | AY.3 | 0.00003 |
S | 816 | S816S | tcA | tcG | 6 | 6 | B.1.243 | 0.000418 |
S | 816 | S816S | tcA | tcT | 6 | 6 | B.1.595 | 0.001566 |
S | 816 | S816S | tcA | tcG | 4 | 5 | AY.113 | 0.00057 |
S | 816 | S816S | tcA | tcT | 1 | 5 | AY.113 | 0.000142 |
S | 816 | S816S | tcA | tcG | 5 | 5 | AY.119 | 0.000177 |
S | 816 | S816S | tcA | tcG | 5 | 5 | AY.39 | 0.000124 |
S | 816 | S816S | tcA | tcG | 4 | 5 | B.1 | 0.000037 |
S | 816 | S816S | tcA | tcT | 1 | 5 | B.1 | 0.000009 |
S | 816 | S816S | tcA | tcG | 4 | 4 | AY.39.1 | 0.000158 |
S | 816 | S816S | tcA | tcG | 4 | 4 | AY.46 | 0.000416 |
S | 816 | S816S | tcA | tcT | 4 | 4 | AY.48 | 0.00186 |
S | 816 | S816S | tcA | tcG | 4 | 4 | AY.98.1 | 0.000194 |
S | 816 | S816S | tcA | tcT | 4 | 4 | B.1.1.70 | 0.001364 |
S | 816 | S816S | tcA | tcT | 2 | 4 | B.1.2 | 0.000018 |
S | 816 | S816S | tcA | tcG | 2 | 4 | B.1.2 | 0.000018 |
S | 816 | S816S | tcA | tcG | 4 | 4 | B.1.36 | 0.000584 |
S | 816 | S816S | tcA | tcG | 3 | 3 | AY.3.1 | 0.000256 |
S | 816 | S816S | tcA | tcC | 2 | 3 | B.1.1.519 | 0.000079 |
S | 816 | S816S | tcA | tcG | 1 | 3 | B.1.1.519 | 0.00004 |
S | 816 | S816S | tcA | tcG | 3 | 3 | B.1.258 | 0.0002 |
S | 816 | S816S | tcA | tcG | 3 | 3 | B.1.526 | 0.000071 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AU.2 | 0.004843 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AY.106 | 0.00067 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AY.109 | 0.001479 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AY.116 | 0.000574 |
S | 816 | S816S | tcA | tcG | 1 | 2 | AY.120 | 0.000037 |
S | 816 | S816S | tcA | tcT | 1 | 2 | AY.120 | 0.000037 |
S | 816 | S816S | tcA | tcG | 1 | 2 | AY.121 | 0.000135 |
S | 816 | S816S | tcA | tcT | 1 | 2 | AY.121 | 0.000135 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AY.2 | 0.000712 |
S | 816 | S816S | tcA | tcG | 1 | 2 | AY.23 | 0.00007 |
S | 816 | S816S | tcA | tcT | 1 | 2 | AY.23 | 0.00007 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AY.32 | 0.001065 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AY.6 | 0.000082 |
S | 816 | S816S | tcA | tcG | 2 | 2 | AY.67 | 0.000929 |
S | 816 | S816S | tcA | tcG | 2 | 2 | B.1.1.311 | 0.000716 |
S | 816 | S816S | tcA | tcG | 2 | 2 | B.1.1.33 | 0.000842 |
S | 816 | S816S | tcA | tcG | 2 | 2 | B.1.177.21 | 0.000153 |
S | 816 | S816S | tcA | tcG | 2 | 2 | B.1.177.44 | 0.001038 |
S | 816 | S816S | tcA | tcG | 2 | 2 | B.1.258.11 | 0.000793 |
S | 816 | S816S | tcA | tcG | 2 | 2 | B.1.351 | 0.000059 |
S | 816 | S816S | tcA | tcG | 2 | 2 | B.1.582 | 0.000981 |
S | 816 | S816S | tcA | tcT | 2 | 2 | P.1.14 | 0.000096 |
S | 816 | S816S | tcA | tcT | 1 | 1 | A.2.5.1 | 0.004808 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.100 | 0.000046 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.108 | 0.001103 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.16 | 0.00038 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.35 | 0.000233 |
S | 816 | S816S | tcA | tcT | 1 | 1 | AY.42 | 0.00004 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.45 | 0.000122 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.46.6 | 0.000072 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.47 | 0.000031 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.5 | 0.000021 |
S | 816 | S816S | tcA | tcT | 1 | 1 | AY.53 | 0.000288 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.68 | 0.000274 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.74 | 0.000116 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.75 | 0.000056 |
S | 816 | S816S | tcA | tcG | 1 | 1 | AY.9.2 | 0.000037 |
S | 816 | S816S | tcA | tcT | 1 | 1 | AY.93 | 0.000273 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.1.207 | 0.001182 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.1.306 | 0.000438 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.1.526 | 0.003546 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.111 | 0.001175 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.177.56 | 0.000668 |
S | 816 | S816S | tcA | tcC | 1 | 1 | B.1.214.2 | 0.0006 |
S | 816 | S816S | tcA | tcC | 1 | 1 | B.1.22 | 0.001318 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.351.2 | 0.000303 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.36.10 | 0.004785 |
S | 816 | S816S | tcA | tcT | 1 | 1 | B.1.36.39 | 0.002217 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.466.2 | 0.000391 |
S | 816 | S816S | tcA | tcT | 1 | 1 | B.1.499 | 0.00105 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.509 | 0.000866 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.558 | 0.004566 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.576 | 0.000907 |
S | 816 | S816S | tcA | tcT | 1 | 1 | B.1.596 | 0.000087 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.1.621.1 | 0.000506 |
S | 816 | S816S | tcA | tcG | 1 | 1 | B.40 | 0.000364 |
S | 816 | S816S | tcA | tcG | 1 | 1 | C.35 | 0.000774 |
S | 816 | S816S | tcA | tcG | 1 | 1 | P.1.1 | 0.000318 |
S | 816 | S816S | tcA | tcT | 1 | 1 | P.1.15 | 0.000232 |
S | 816 | S816S | tcA | tcG | 1 | 1 | P.1.17 | 0.000162 |
S | 816 | S816S | tcA | tcG | 1 | 1 | P.2 | 0.000187 |
S | 816 | S816S | tcA | tcG | 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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