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 | 190 | R190S | nonsyn | agG | agT | 108614 | 108611 | 0.999972 | 22130-22132 |
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 |
S | 190 | R190S | agG | agT | 108611 | 108614 | All | 0.020773 |
S | 190 | R190S | agG | agT | 59413 | 59413 | P.1 | 0.935992 |
S | 190 | R190S | agG | agT | 20417 | 20417 | P.1.14 | 0.975956 |
S | 190 | R190S | agG | agT | 5750 | 5750 | P.1.17 | 0.93012 |
S | 190 | R190S | agG | agT | 3843 | 3843 | P.1.15 | 0.89289 |
S | 190 | R190S | agG | agT | 3358 | 3358 | P.1.10 | 0.904877 |
S | 190 | R190S | agG | agT | 3045 | 3045 | P.1.7 | 0.972222 |
S | 190 | R190S | agG | agT | 2809 | 2809 | P.1.1 | 0.892313 |
S | 190 | R190S | agG | agT | 2410 | 2410 | P.1.16 | 0.901609 |
S | 190 | R190S | agG | agT | 1644 | 1644 | P.1.12 | 0.795741 |
S | 190 | R190S | agG | agT | 1137 | 1137 | P.1.17.1 | 0.994751 |
S | 190 | R190S | agG | agT | 998 | 998 | P.1.4 | 0.974609 |
S | 190 | R190S | agG | agT | 852 | 852 | P.1.13 | 0.765499 |
S | 190 | R190S | agG | agT | 829 | 829 | P.1.2 | 0.958382 |
S | 190 | R190S | agG | agT | 504 | 504 | P.1.6 | 0.980545 |
S | 190 | R190S | agG | agT | 234 | 234 | A.21 | 0.648199 |
S | 190 | R190S | agG | agT | 227 | 227 | C.1.2 | 0.965957 |
S | 190 | R190S | agG | agT | 200 | 200 | P.1.9 | 0.961538 |
S | 190 | R190S | agG | agT | 199 | 199 | P.1.8 | 0.952153 |
S | 190 | R190S | agG | agT | 95 | 95 | P.1.10.1 | 0.772358 |
S | 190 | R190S | agG | agT | 89 | 89 | P.1.11 | 0.908163 |
S | 190 | R190S | agG | agT | 55 | 55 | B.1 | 0.000504 |
S | 190 | R190S | agG | agT | 48 | 48 | B.1.1.7 | 0.000043 |
S | 190 | R190S | agG | agT | 39 | 39 | B.1.1 | 0.000707 |
S | 190 | R190S | agG | agT | 32 | 32 | C.36.3.1 | 0.086957 |
S | 190 | R190S | agG | agT | 28 | 28 | P.1.3 | 0.965517 |
S | 190 | R190S | agG | agT | 24 | 24 | B.1.1.528 | 0.115385 |
S | 190 | R190S | agG | agT | 24 | 24 | P.1.10.2 | 1 |
S | 190 | R190S | agG | agT | 21 | 21 | B.1.576 | 0.019039 |
S | 190 | R190S | agG | agT | 21 | 21 | B.1.617.2 | 0.000079 |
S | 190 | R190S | agG | agT | 20 | 20 | AY.99.2 | 0.001843 |
S | 190 | R190S | agG | agT | 15 | 16 | AY.4 | 0.000023 |
S | 190 | R190S | agG | agT | 15 | 15 | B.1.214.2 | 0.008993 |
S | 190 | R190S | agG | agT | 14 | 14 | C.37 | 0.001625 |
S | 190 | R190S | agG | agT | 13 | 13 | P.1.5 | 1 |
S | 190 | R190S | agG | agT | 12 | 12 | AY.39 | 0.000297 |
S | 190 | R190S | agG | agT | 10 | 10 | B.1.243 | 0.000696 |
S | 190 | R190S | agG | agT | 9 | 9 | AY.43 | 0.00004 |
S | 190 | R190S | agG | agT | 9 | 9 | AY.44 | 0.000055 |
S | 190 | R190S | agG | agT | 8 | 8 | AY.25 | 0.000048 |
S | 190 | R190S | agG | agT | 7 | 7 | A.2.5 | 0.003493 |
S | 190 | R190S | agG | agT | 6 | 6 | B | 0.000767 |
S | 190 | R190S | agG | agT | 6 | 6 | B.1.427 | 0.000303 |
S | 190 | R190S | agG | agT | 5 | 5 | B.1.1.161 | 0.017668 |
S | 190 | R190S | agG | agT | 5 | 5 | B.1.1.28 | 0.001556 |
S | 190 | R190S | agG | agT | 5 | 5 | B.1.396 | 0.003529 |
S | 190 | R190S | agG | agT | 4 | 4 | AY.103 | 0.000025 |
S | 190 | R190S | agG | agT | 4 | 4 | AY.34.1 | 0.00204 |
S | 190 | R190S | agG | agT | 4 | 4 | AY.5 | 0.000083 |
S | 190 | R190S | agG | agT | 4 | 4 | AY.9.2 | 0.000147 |
S | 190 | R190S | agG | agT | 4 | 4 | B.1.351 | 0.000119 |
S | 190 | R190S | agG | agT | 4 | 4 | N.5 | 0.007067 |
S | 190 | R190S | agG | agT | 3 | 3 | AY.121 | 0.000406 |
S | 190 | R190S | agG | agT | 3 | 3 | AY.68 | 0.000821 |
S | 190 | R190S | agG | agT | 3 | 3 | B.1.1.317 | 0.001235 |
S | 190 | R190S | agG | agT | 3 | 3 | B.1.2 | 0.000026 |
S | 190 | R190S | agG | agT | 3 | 3 | B.1.596 | 0.000261 |
S | 190 | R190S | agG | agT | 3 | 3 | B.1.636 | 0.020134 |
S | 190 | R190S | agG | agT | 3 | 3 | Q.1 | 0.000379 |
S | 190 | R190S | agG | agT | 2 | 2 | A | 0.000774 |
S | 190 | R190S | agG | agT | 2 | 2 | AY.45 | 0.000243 |
S | 190 | R190S | agG | agT | 2 | 2 | AY.75 | 0.000112 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.1.1 | 0.000653 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.1.368 | 0.006173 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.177.86 | 0.000367 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.429 | 0.000047 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.526 | 0.000047 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.575 | 0.000607 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.621 | 0.000177 |
S | 190 | R190S | agG | agT | 2 | 2 | B.1.637 | 0.000146 |
S | 190 | R190S | agG | agT | 2 | 2 | C.1 | 0.004785 |
S | 190 | R190S | agG | agT | 1 | 1 | A.18 | 0.05 |
S | 190 | R190S | agG | agT | 1 | 1 | A.2 | 0.000662 |
S | 190 | R190S | agG | agT | 1 | 1 | A.2.5.1 | 0.004808 |
S | 190 | R190S | agG | agT | 1 | 1 | A.3 | 0.002096 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.100 | 0.000046 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.102 | 0.000027 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.111 | 0.000183 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.116 | 0.000287 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.116.1 | 0.000311 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.118 | 0.000063 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.23 | 0.00007 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.26 | 0.000028 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.3 | 0.00001 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.32 | 0.000532 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.38 | 0.000499 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.39.1 | 0.00004 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.4.2 | 0.000022 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.46.3 | 0.000934 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.69 | 0.000187 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.92 | 0.000287 |
S | 190 | R190S | agG | agT | 1 | 1 | AY.98.1 | 0.000048 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.1.220 | 0.001859 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.1.519 | 0.00004 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.177 | 0.000013 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.177.73 | 0.000566 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.177.83 | 0.001481 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.214 | 0.003663 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.311 | 0.000275 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.349 | 0.000715 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.36.16 | 0.001425 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.36.37 | 0.002778 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.399 | 0.001934 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.533 | 0.009615 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.623 | 0.000536 |
S | 190 | R190S | agG | agT | 1 | 1 | B.1.635 | 0.017544 |
S | 190 | R190S | agG | agT | 1 | 1 | C.35 | 0.000774 |
S | 190 | R190S | agG | agT | 1 | 1 | P.4 | 0.003802 |
S | 190 | R190S | agG | agT | 1 | 1 | P.7 | 0.004367 |
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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