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/nsp12 | 562 | I562I | I4954I | syn | atC | atT | 508 | 422 | 0.830709 | 15124-15126 |
ORF1ab/nsp12 | 562 | I562I | I4954I | syn | atC | atA | 508 | 86 | 0.169291 | 15124-15126 |
Details of the mutation I562I 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/nsp12 | 562 | I562I | atC | atT | 422 | 508 | All | 0.000081 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 86 | 508 | All | 0.000016 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 77 | 90 | B.1.1.7 | 0.000069 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 13 | 90 | B.1.1.7 | 0.000012 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 36 | 41 | P.1.14 | 0.001721 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 5 | 41 | P.1.14 | 0.000239 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 37 | 37 | B.1.177 | 0.000487 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 27 | 27 | AY.25 | 0.000162 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 27 | 27 | B.1.2 | 0.000238 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 21 | 25 | AY.4 | 0.000033 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 4 | 25 | AY.4 | 0.000006 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 20 | 21 | B.1.617.2 | 0.000075 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 21 | B.1.617.2 | 0.000004 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 19 | 19 | A.18 | 0.95 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 16 | 18 | B.1 | 0.000147 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 2 | 18 | B.1 | 0.000018 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 18 | 18 | B.1.160 | 0.000561 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 9 | 13 | AY.43 | 0.00004 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 4 | 13 | AY.43 | 0.000018 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 7 | 10 | B.1.525 | 0.000792 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 3 | 10 | B.1.525 | 0.000339 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 8 | 9 | AY.3 | 0.00008 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 9 | AY.3 | 0.00001 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 6 | 9 | AY.44 | 0.000037 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 3 | 9 | AY.44 | 0.000018 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 9 | 9 | B.1.1.316 | 0.008326 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 8 | 8 | B.1.177.81 | 0.001515 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 7 | 7 | B.1.1 | 0.000127 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 6 | 6 | AY.73 | 0.003992 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 6 | 6 | P.1 | 0.000095 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 4 | 5 | AY.103 | 0.000025 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 5 | AY.103 | 0.000006 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 5 | 5 | AY.4.2 | 0.000108 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 5 | 5 | AY.5 | 0.000103 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 5 | 5 | C.37 | 0.00058 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 4 | 4 | B.1.36.17 | 0.001976 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 3 | 3 | A.21 | 0.00831 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 3 | 3 | AY.120 | 0.000112 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 3 | 3 | AY.29 | 0.000047 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 2 | 3 | AY.6 | 0.000082 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 3 | AY.6 | 0.000041 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 3 | 3 | B.1.1.253 | 0.007519 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 3 | 3 | B.1.232 | 0.001612 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 2 | 3 | B.1.429 | 0.000047 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 3 | B.1.429 | 0.000024 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 2 | A.1 | 0.000282 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 2 | A.1 | 0.000282 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | A.19 | 0.018868 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 2 | AY.20 | 0.000039 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 2 | AY.20 | 0.000039 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | AY.9.2.1 | 0.003953 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | AY.98.1 | 0.000097 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | B.1.1.70 | 0.000682 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | B.1.177.4 | 0.000422 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | B.1.258 | 0.000133 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | B.1.36.7 | 0.008 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 2 | B.1.612 | 0.002653 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 2 | B.1.612 | 0.002653 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 2 | 2 | R.1 | 0.00018 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 1 | 0.055556 | |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | A | 0.000387 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | A.2.5 | 0.000499 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.111 | 0.000183 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.34 | 0.000097 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 1 | AY.40 | 0.000964 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.46.5 | 0.000198 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.47 | 0.000031 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 1 | AY.7.1 | 0.000113 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | AY.98 | 0.000079 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.1.222 | 0.000204 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.1.37 | 0.000193 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.126 | 0.001276 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.177.33 | 0.001645 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 1 | B.1.177.73 | 0.000566 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.234 | 0.000132 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.240 | 0.000216 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.390 | 0.010638 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.438.1 | 0.000107 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.560 | 0.00463 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.575 | 0.000303 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.1.619.1 | 0.000641 |
ORF1ab/nsp12 | 562 | I562I | atC | atA | 1 | 1 | B.1.636 | 0.006711 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | B.47 | 0.020408 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | C.1 | 0.002392 |
ORF1ab/nsp12 | 562 | I562I | atC | atT | 1 | 1 | P.6 | 0.003145 |
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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