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 | 109 | P109P | P109P | syn | ccT | ccC | 3536 | 2362 | 0.667986 | 590-592 |
ORF1ab/nsp1 | 109 | P109P | P109P | syn | ccT | ccA | 3536 | 1119 | 0.316459 | 590-592 |
ORF1ab/nsp1 | 109 | P109P | P109P | syn | ccT | ccG | 3536 | 55 | 0.0155543 | 590-592 |
Details of the mutation P109P 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 | 109 | P109P | ccT | ccC | 2362 | 3536 | All | 0.000452 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1119 | 3536 | All | 0.000214 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 55 | 3536 | All | 0.000011 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1197 | 1197 | P.1 | 0.018858 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1032 | 1040 | AY.3 | 0.010265 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 6 | 1040 | AY.3 | 0.00006 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 2 | 1040 | AY.3 | 0.00002 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 209 | 209 | P.1.8 | 1 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 202 | 202 | P.1.9 | 0.971154 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 152 | 160 | B.1.1.7 | 0.000136 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 6 | 160 | B.1.1.7 | 0.000005 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 2 | 160 | B.1.1.7 | 0.000002 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 152 | 152 | AY.101 | 0.074546 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 30 | 56 | B.1.617.2 | 0.000113 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 25 | 56 | B.1.617.2 | 0.000094 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 1 | 56 | B.1.617.2 | 0.000004 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 39 | 53 | AY.43 | 0.000173 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 14 | 53 | AY.43 | 0.000062 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 48 | 51 | AY.4 | 0.000075 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 3 | 51 | AY.4 | 0.000005 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 26 | 39 | AY.44 | 0.000158 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 9 | 39 | AY.44 | 0.000055 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 4 | 39 | AY.44 | 0.000024 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 32 | 32 | B.1.280 | 0.228571 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 29 | 30 | AY.25 | 0.000174 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 30 | AY.25 | 0.000006 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 16 | 22 | B.1.2 | 0.000141 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 4 | 22 | B.1.2 | 0.000035 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 2 | 22 | B.1.2 | 0.000018 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 12 | 19 | AY.103 | 0.000075 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 5 | 19 | AY.103 | 0.000031 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 2 | 19 | AY.103 | 0.000012 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 18 | 18 | P.1.12 | 0.008712 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 17 | 17 | B.1.177.12 | 0.002579 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 14 | 14 | B.1.110.3 | 0.010057 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 10 | 11 | B.1.1 | 0.000181 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 11 | B.1.1 | 0.000018 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 8 | 9 | B.1 | 0.000073 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 9 | B.1 | 0.000009 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 9 | 9 | B.1.429 | 0.000212 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 8 | 8 | AY.100 | 0.000368 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 8 | 8 | B.1.1.301 | 0.009434 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 5 | 8 | B.1.177 | 0.000066 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 2 | 8 | B.1.177 | 0.000026 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 8 | B.1.177 | 0.000013 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 8 | 8 | B.3 | 0.006645 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 4 | 7 | AY.118 | 0.000251 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 3 | 7 | AY.118 | 0.000188 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 6 | 7 | AY.5.3 | 0.002024 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 7 | AY.5.3 | 0.000337 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 4 | 7 | B.1.637 | 0.000292 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 7 | B.1.637 | 0.000219 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 6 | 6 | B.1.1.303 | 0.016575 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 5 | 5 | P.1.14 | 0.000239 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 4 | AY.102 | 0.00008 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 4 | AY.102 | 0.000027 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 4 | 4 | AY.119 | 0.000141 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 4 | 4 | AY.20 | 0.000155 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 4 | 4 | AY.27 | 0.000259 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 3 | 4 | AY.39 | 0.000074 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 4 | AY.39 | 0.000025 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 3 | 4 | AY.5 | 0.000062 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 4 | AY.5 | 0.000021 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 4 | 4 | B.1.210 | 0.008529 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 4 | 4 | P.1.13 | 0.003594 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 3 | 3 | AY.114 | 0.000693 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 2 | 3 | AY.23 | 0.000139 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 3 | AY.23 | 0.00007 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | AY.26 | 0.000085 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 3 | AY.45 | 0.000243 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 3 | AY.45 | 0.000122 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 3 | AY.46 | 0.000208 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 3 | AY.46 | 0.000104 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | AY.46.2 | 0.001906 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | AY.6 | 0.000123 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | AY.65 | 0.001599 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | B.1.160 | 0.000094 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | B.1.427 | 0.000151 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 3 | B.1.526 | 0.000047 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 1 | 3 | B.1.526 | 0.000024 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | B.1.575 | 0.00091 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 2 | 3 | B.1.621 | 0.000177 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 3 | B.1.621 | 0.000089 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 3 | 3 | P.1.16 | 0.001122 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 2 | AY.24 | 0.000862 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 2 | 2 | AY.30 | 0.000791 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 2 | AY.4.2 | 0.000043 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 2 | AY.50 | 0.001599 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 2 | AZ.3 | 0.00304 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 2 | B.1.177.7 | 0.00033 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 1 | 2 | B.1.596 | 0.000087 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 2 | B.1.596 | 0.000087 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 2 | C.37 | 0.000116 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 2 | C.37 | 0.000116 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 2 | 2 | P.1.1 | 0.000635 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 1 | 1 | 0.055556 | |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | AY.39.2 | 0.001541 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.4.3 | 0.000842 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.92 | 0.000287 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | AY.96 | 0.002075 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.1.294 | 0.001266 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccA | 1 | 1 | B.1.1.50 | 0.000679 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.177.33 | 0.001645 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.311 | 0.000275 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.401 | 0.008197 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.582 | 0.000491 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.597 | 0.00463 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | B.1.617.1 | 0.000129 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | C.37.1 | 0.002618 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | P.1.15 | 0.000232 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccG | 1 | 1 | P.1.17 | 0.000162 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | P.1.7 | 0.000319 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | P.2 | 0.000187 |
ORF1ab/nsp1 | 109 | P109P | ccT | ccC | 1 | 1 | Q.8 | 0.000165 |
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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