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 | 1198 | I1198I | syn | atC | atT | 1955 | 1903 | 0.973402 | 25154-25156 | |
S | 1198 | I1198I | syn | atC | atA | 1955 | 52 | 0.0265985 | 25154-25156 |
Details of the mutation I1198I 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 | 1198 | I1198I | atC | atT | 1903 | 1955 | All | 0.000364 |
S | 1198 | I1198I | atC | atA | 52 | 1955 | All | 0.00001 |
S | 1198 | I1198I | atC | atT | 413 | 413 | B.1.2 | 0.003637 |
S | 1198 | I1198I | atC | atT | 246 | 246 | B.1.617.2 | 0.000926 |
S | 1198 | I1198I | atC | atT | 169 | 202 | B.1.1.7 | 0.000151 |
S | 1198 | I1198I | atC | atA | 33 | 202 | B.1.1.7 | 0.00003 |
S | 1198 | I1198I | atC | atT | 137 | 138 | AY.25 | 0.000824 |
S | 1198 | I1198I | atC | atA | 1 | 138 | AY.25 | 0.000006 |
S | 1198 | I1198I | atC | atT | 113 | 113 | AY.39.1 | 0.004476 |
S | 1198 | I1198I | atC | atT | 102 | 102 | AY.43 | 0.000452 |
S | 1198 | I1198I | atC | atT | 69 | 75 | AY.4 | 0.000107 |
S | 1198 | I1198I | atC | atA | 6 | 75 | AY.4 | 0.000009 |
S | 1198 | I1198I | atC | atT | 50 | 50 | B.1.221 | 0.003552 |
S | 1198 | I1198I | atC | atT | 39 | 40 | AY.103 | 0.000242 |
S | 1198 | I1198I | atC | atA | 1 | 40 | AY.103 | 0.000006 |
S | 1198 | I1198I | atC | atT | 34 | 34 | AY.44 | 0.000207 |
S | 1198 | I1198I | atC | atT | 23 | 27 | B.1 | 0.000211 |
S | 1198 | I1198I | atC | atA | 4 | 27 | B.1 | 0.000037 |
S | 1198 | I1198I | atC | atT | 24 | 25 | AY.102 | 0.000636 |
S | 1198 | I1198I | atC | atA | 1 | 25 | AY.102 | 0.000027 |
S | 1198 | I1198I | atC | atT | 23 | 23 | M.1 | 0.534884 |
S | 1198 | I1198I | atC | atT | 22 | 22 | AY.3 | 0.000219 |
S | 1198 | I1198I | atC | atT | 22 | 22 | B.1.177 | 0.00029 |
S | 1198 | I1198I | atC | atT | 20 | 21 | B.1.596 | 0.001743 |
S | 1198 | I1198I | atC | atA | 1 | 21 | B.1.596 | 0.000087 |
S | 1198 | I1198I | atC | atT | 19 | 19 | B.1.526 | 0.000447 |
S | 1198 | I1198I | atC | atT | 17 | 18 | B.1.351 | 0.000505 |
S | 1198 | I1198I | atC | atA | 1 | 18 | B.1.351 | 0.00003 |
S | 1198 | I1198I | atC | atT | 18 | 18 | B.1.429 | 0.000424 |
S | 1198 | I1198I | atC | atT | 17 | 17 | AY.26 | 0.000481 |
S | 1198 | I1198I | atC | atT | 17 | 17 | AY.39 | 0.00042 |
S | 1198 | I1198I | atC | atT | 16 | 16 | B.1.160 | 0.000499 |
S | 1198 | I1198I | atC | atT | 14 | 14 | P.1 | 0.000221 |
S | 1198 | I1198I | atC | atT | 13 | 13 | AY.118 | 0.000814 |
S | 1198 | I1198I | atC | atT | 13 | 13 | AY.5 | 0.000268 |
S | 1198 | I1198I | atC | atT | 10 | 10 | AY.100 | 0.00046 |
S | 1198 | I1198I | atC | atT | 9 | 9 | AY.110 | 0.001014 |
S | 1198 | I1198I | atC | atT | 9 | 9 | B.1.1 | 0.000163 |
S | 1198 | I1198I | atC | atT | 9 | 9 | B.1.1.269 | 0.012179 |
S | 1198 | I1198I | atC | atT | 7 | 7 | AY.117 | 0.000592 |
S | 1198 | I1198I | atC | atT | 7 | 7 | AY.120 | 0.00026 |
S | 1198 | I1198I | atC | atT | 7 | 7 | AY.27 | 0.000453 |
S | 1198 | I1198I | atC | atT | 7 | 7 | AY.42 | 0.000282 |
S | 1198 | I1198I | atC | atT | 7 | 7 | AY.46 | 0.000729 |
S | 1198 | I1198I | atC | atT | 7 | 7 | B.1.1.222 | 0.001428 |
S | 1198 | I1198I | atC | atT | 7 | 7 | B.1.568 | 0.007778 |
S | 1198 | I1198I | atC | atT | 7 | 7 | B.1.595 | 0.001827 |
S | 1198 | I1198I | atC | atT | 6 | 6 | B.1.243 | 0.000418 |
S | 1198 | I1198I | atC | atT | 6 | 6 | R.1 | 0.00054 |
S | 1198 | I1198I | atC | atT | 5 | 5 | AY.20 | 0.000194 |
S | 1198 | I1198I | atC | atT | 5 | 5 | B.1.1.28 | 0.001556 |
S | 1198 | I1198I | atC | atT | 5 | 5 | B.1.1.519 | 0.000199 |
S | 1198 | I1198I | atC | atT | 5 | 5 | B.1.177.46 | 0.004591 |
S | 1198 | I1198I | atC | atT | 5 | 5 | N.9 | 0.029762 |
S | 1198 | I1198I | atC | atT | 4 | 4 | AY.119 | 0.000141 |
S | 1198 | I1198I | atC | atT | 4 | 4 | B.1.1.434 | 0.001394 |
S | 1198 | I1198I | atC | atT | 4 | 4 | B.1.621 | 0.000354 |
S | 1198 | I1198I | atC | atT | 4 | 4 | P.1.14 | 0.000191 |
S | 1198 | I1198I | atC | atT | 3 | 3 | AY.23 | 0.000209 |
S | 1198 | I1198I | atC | atT | 3 | 3 | AY.29 | 0.000047 |
S | 1198 | I1198I | atC | atT | 3 | 3 | AY.45 | 0.000365 |
S | 1198 | I1198I | atC | atT | 3 | 3 | AY.46.6 | 0.000217 |
S | 1198 | I1198I | atC | atT | 3 | 3 | AY.48 | 0.001395 |
S | 1198 | I1198I | atC | atT | 3 | 3 | AY.6 | 0.000123 |
S | 1198 | I1198I | atC | atT | 3 | 3 | AY.88 | 0.002653 |
S | 1198 | I1198I | atC | atT | 3 | 3 | B.1.1.214 | 0.000166 |
S | 1198 | I1198I | atC | atT | 3 | 3 | B.1.258.17 | 0.000312 |
S | 1198 | I1198I | atC | atT | 3 | 3 | B.1.36.29 | 0.001552 |
S | 1198 | I1198I | atC | atT | 3 | 3 | B.1.400 | 0.001287 |
S | 1198 | I1198I | atC | atA | 2 | 3 | B.1.427 | 0.000101 |
S | 1198 | I1198I | atC | atT | 1 | 3 | B.1.427 | 0.00005 |
S | 1198 | I1198I | atC | atT | 3 | 3 | C.30 | 0.005181 |
S | 1198 | I1198I | atC | atT | 3 | 3 | P.2 | 0.00056 |
S | 1198 | I1198I | atC | atT | 2 | 2 | AY.12 | 0.000632 |
S | 1198 | I1198I | atC | atT | 2 | 2 | AY.14 | 0.000176 |
S | 1198 | I1198I | atC | atT | 2 | 2 | AY.24 | 0.000862 |
S | 1198 | I1198I | atC | atT | 2 | 2 | AY.46.4 | 0.000329 |
S | 1198 | I1198I | atC | atT | 2 | 2 | AY.59 | 0.001059 |
S | 1198 | I1198I | atC | atT | 2 | 2 | AY.75 | 0.000112 |
S | 1198 | I1198I | atC | atT | 2 | 2 | AY.92 | 0.000575 |
S | 1198 | I1198I | atC | atT | 2 | 2 | B.1.1.113 | 0.013986 |
S | 1198 | I1198I | atC | atT | 2 | 2 | B.1.1.241 | 0.004141 |
S | 1198 | I1198I | atC | atT | 2 | 2 | B.1.1.311 | 0.000716 |
S | 1198 | I1198I | atC | atT | 2 | 2 | B.1.177.21 | 0.000153 |
S | 1198 | I1198I | atC | atT | 2 | 2 | B.1.189 | 0.008584 |
S | 1198 | I1198I | atC | atT | 2 | 2 | B.1.326 | 0.015152 |
S | 1198 | I1198I | atC | atT | 2 | 2 | B.1.36 | 0.000292 |
S | 1198 | I1198I | atC | atT | 2 | 2 | C.36.3 | 0.001134 |
S | 1198 | I1198I | atC | atT | 1 | 1 | 0.055556 | |
S | 1198 | I1198I | atC | atT | 1 | 1 | A.23.1 | 0.000704 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.116 | 0.000287 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.16 | 0.00038 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.2 | 0.000356 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.34 | 0.000097 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.4.2 | 0.000022 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.5.4 | 0.000277 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.51 | 0.000909 |
S | 1198 | I1198I | atC | atA | 1 | 1 | AY.55 | 0.000917 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.65 | 0.000533 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.74 | 0.000116 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.80 | 0.001129 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.98 | 0.000079 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.98.1 | 0.000048 |
S | 1198 | I1198I | atC | atT | 1 | 1 | AY.99.2 | 0.000092 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B | 0.000128 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.1.216 | 0.00089 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.1.294 | 0.001266 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.1.306 | 0.000438 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.1.318 | 0.000302 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.1.420 | 0.001006 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.177.38 | 0.010417 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.177.73 | 0.000566 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.23 | 0.006061 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.258 | 0.000067 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.306 | 0.005714 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.36.38 | 0.001642 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.438.1 | 0.000107 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.493 | 0.025641 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.525 | 0.000113 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.607 | 0.052632 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.612 | 0.002653 |
S | 1198 | I1198I | atC | atA | 1 | 1 | B.1.617.1 | 0.000129 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.1.620 | 0.000946 |
S | 1198 | I1198I | atC | atT | 1 | 1 | B.23 | 0.002924 |
S | 1198 | I1198I | atC | atT | 1 | 1 | C.35 | 0.000774 |
S | 1198 | I1198I | atC | atT | 1 | 1 | P.1.12 | 0.000484 |
S | 1198 | I1198I | atC | atT | 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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