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/nsp2 | 4 | R4H | R184H | nonsyn | cGc | cAc | 644 | 643 | 0.998447 | 815-817 |
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 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 643 | 644 | All | 0.000123 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 213 | 213 | B.1.1.7 | 0.000191 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 44 | 45 | AY.43 | 0.000195 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 42 | 42 | AY.4 | 0.000065 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 38 | 38 | B.1.617.2 | 0.000143 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 34 | 34 | B.1.2 | 0.000299 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 24 | 24 | AY.25 | 0.000144 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 24 | 24 | AY.44 | 0.000146 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 14 | 14 | AY.20 | 0.000544 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 10 | 10 | AY.3 | 0.000099 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 10 | 10 | B.1.177 | 0.000132 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 9 | 9 | AY.5 | 0.000186 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 8 | 8 | B.1.177.15 | 0.005047 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 8 | 8 | P.1 | 0.000126 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 7 | 7 | B.1.234 | 0.000924 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 7 | 7 | B.1.258 | 0.000466 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | AY.100 | 0.000276 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | AY.103 | 0.000037 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | AY.9.1 | 0.000502 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | B.1 | 0.000055 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | B.1.1.214 | 0.000333 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | B.1.1.420 | 0.006036 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | B.1.526 | 0.000141 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 6 | 6 | B.1.621 | 0.000531 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 5 | 5 | AY.4.2 | 0.000108 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 5 | 5 | AY.61 | 0.000524 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 5 | 5 | B.1.351 | 0.000149 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 4 | 4 | AY.118 | 0.000251 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 4 | 4 | AY.65 | 0.002132 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 4 | 4 | B.1.1 | 0.000073 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 3 | 3 | AY.29 | 0.000047 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 3 | 3 | AY.62 | 0.001307 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 3 | 3 | B.1.1.28 | 0.000934 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 3 | 3 | B.1.427 | 0.000151 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.102 | 0.000053 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.113 | 0.000285 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.23 | 0.000139 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.42 | 0.00008 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | AY.45 | 0.000243 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | B.1.1.337 | 0.007194 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | B.1.400 | 0.000858 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | A.1 | 0.000282 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | A.23.1 | 0.000704 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | A.5 | 0.001923 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.105 | 0.000643 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.106 | 0.000335 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.116 | 0.000287 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.120.1 | 0.000321 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.35 | 0.000233 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.41 | 0.000294 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.52 | 0.000814 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.55 | 0.000917 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.73 | 0.000665 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.90 | 0.000684 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.1.354 | 0.004386 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.105 | 0.009615 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.221.4 | 0.004167 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.232 | 0.000537 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.265 | 0.001271 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.36 | 0.000146 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.517 | 0.000427 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.556 | 0.007519 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | B.1.609 | 0.000479 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 1 | 1 | N.4 | 0.004255 |
ORF1ab/nsp2 | 4 | R4H | cGc | cAc | 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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