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 | 980 | I980I | syn | atC | atT | 1875 | 1520 | 0.810667 | 24500-24502 | |
S | 980 | I980I | syn | atC | atA | 1875 | 355 | 0.189333 | 24500-24502 |
Details of the mutation I980I 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 | 980 | I980I | atC | atT | 1520 | 1875 | All | 0.000291 |
S | 980 | I980I | atC | atA | 355 | 1875 | All | 0.000068 |
S | 980 | I980I | atC | atT | 820 | 973 | B.1.1.7 | 0.000734 |
S | 980 | I980I | atC | atA | 153 | 973 | B.1.1.7 | 0.000137 |
S | 980 | I980I | atC | atT | 136 | 136 | B.1.160 | 0.004242 |
S | 980 | I980I | atC | atT | 78 | 123 | AY.4 | 0.000121 |
S | 980 | I980I | atC | atA | 45 | 123 | AY.4 | 0.00007 |
S | 980 | I980I | atC | atA | 101 | 101 | B.1.1.380 | 0.990196 |
S | 980 | I980I | atC | atT | 65 | 68 | B.1 | 0.000595 |
S | 980 | I980I | atC | atA | 3 | 68 | B.1 | 0.000027 |
S | 980 | I980I | atC | atT | 60 | 61 | B.1.2 | 0.000528 |
S | 980 | I980I | atC | atA | 1 | 61 | B.1.2 | 0.000009 |
S | 980 | I980I | atC | atT | 34 | 47 | AY.103 | 0.000211 |
S | 980 | I980I | atC | atA | 13 | 47 | AY.103 | 0.000081 |
S | 980 | I980I | atC | atT | 31 | 38 | B.1.617.2 | 0.000117 |
S | 980 | I980I | atC | atA | 7 | 38 | B.1.617.2 | 0.000026 |
S | 980 | I980I | atC | atT | 32 | 32 | P.1.10 | 0.008623 |
S | 980 | I980I | atC | atT | 13 | 20 | B.1.429 | 0.000306 |
S | 980 | I980I | atC | atA | 7 | 20 | B.1.429 | 0.000165 |
S | 980 | I980I | atC | atT | 17 | 17 | B.1.621 | 0.001505 |
S | 980 | I980I | atC | atT | 11 | 11 | B.1.596 | 0.000959 |
S | 980 | I980I | atC | atT | 10 | 11 | Q.1 | 0.001263 |
S | 980 | I980I | atC | atA | 1 | 11 | Q.1 | 0.000126 |
S | 980 | I980I | atC | atT | 9 | 10 | AY.30 | 0.003562 |
S | 980 | I980I | atC | atA | 1 | 10 | AY.30 | 0.000396 |
S | 980 | I980I | atC | atT | 9 | 10 | AY.43 | 0.00004 |
S | 980 | I980I | atC | atA | 1 | 10 | AY.43 | 0.000004 |
S | 980 | I980I | atC | atT | 10 | 10 | AY.46.4 | 0.001645 |
S | 980 | I980I | atC | atT | 9 | 9 | AY.3 | 0.00009 |
S | 980 | I980I | atC | atT | 9 | 9 | B.1.361 | 0.011598 |
S | 980 | I980I | atC | atT | 7 | 8 | AY.44 | 0.000043 |
S | 980 | I980I | atC | atA | 1 | 8 | AY.44 | 0.000006 |
S | 980 | I980I | atC | atT | 7 | 8 | B.1.177 | 0.000092 |
S | 980 | I980I | atC | atA | 1 | 8 | B.1.177 | 0.000013 |
S | 980 | I980I | atC | atT | 8 | 8 | B.1.526 | 0.000188 |
S | 980 | I980I | atC | atT | 5 | 7 | AY.102 | 0.000133 |
S | 980 | I980I | atC | atA | 2 | 7 | AY.102 | 0.000053 |
S | 980 | I980I | atC | atT | 6 | 7 | AY.20 | 0.000233 |
S | 980 | I980I | atC | atA | 1 | 7 | AY.20 | 0.000039 |
S | 980 | I980I | atC | atT | 6 | 7 | B.1.1 | 0.000109 |
S | 980 | I980I | atC | atA | 1 | 7 | B.1.1 | 0.000018 |
S | 980 | I980I | atC | atT | 7 | 7 | B.1.404 | 0.009115 |
S | 980 | I980I | atC | atT | 5 | 5 | AY.25 | 0.00003 |
S | 980 | I980I | atC | atT | 5 | 5 | B.1.243 | 0.000348 |
S | 980 | I980I | atC | atT | 5 | 5 | B.1.595 | 0.001305 |
S | 980 | I980I | atC | atT | 3 | 5 | P.1 | 0.000047 |
S | 980 | I980I | atC | atA | 2 | 5 | P.1 | 0.000032 |
S | 980 | I980I | atC | atT | 4 | 4 | AY.26 | 0.000113 |
S | 980 | I980I | atC | atT | 3 | 4 | AY.39 | 0.000074 |
S | 980 | I980I | atC | atA | 1 | 4 | AY.39 | 0.000025 |
S | 980 | I980I | atC | atA | 4 | 4 | B.1.177.57 | 0.001124 |
S | 980 | I980I | atC | atT | 4 | 4 | B.1.351 | 0.000119 |
S | 980 | I980I | atC | atT | 3 | 3 | AY.4.2 | 0.000065 |
S | 980 | I980I | atC | atT | 3 | 3 | AY.47 | 0.000093 |
S | 980 | I980I | atC | atT | 3 | 3 | AY.98 | 0.000237 |
S | 980 | I980I | atC | atA | 3 | 3 | B.1.1.28 | 0.000934 |
S | 980 | I980I | atC | atT | 3 | 3 | B.1.1.309 | 0.017544 |
S | 980 | I980I | atC | atT | 3 | 3 | B.1.206 | 0.002447 |
S | 980 | I980I | atC | atT | 3 | 3 | N.4 | 0.012766 |
S | 980 | I980I | atC | atT | 3 | 3 | P.1.2 | 0.003468 |
S | 980 | I980I | atC | atT | 2 | 2 | A.2.5 | 0.000998 |
S | 980 | I980I | atC | atT | 2 | 2 | AY.119 | 0.000071 |
S | 980 | I980I | atC | atA | 2 | 2 | AY.16 | 0.000759 |
S | 980 | I980I | atC | atA | 1 | 2 | AY.39.1 | 0.00004 |
S | 980 | I980I | atC | atT | 1 | 2 | AY.39.1 | 0.00004 |
S | 980 | I980I | atC | atT | 2 | 2 | AY.9.2 | 0.000073 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.1.434 | 0.000697 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.1.63 | 0.000772 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.111 | 0.00235 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.258.17 | 0.000208 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.330 | 0.057143 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.369 | 0.00057 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.427 | 0.000101 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.517 | 0.000854 |
S | 980 | I980I | atC | atA | 2 | 2 | B.1.609 | 0.000959 |
S | 980 | I980I | atC | atT | 2 | 2 | B.1.78 | 0.017094 |
S | 980 | I980I | atC | atT | 2 | 2 | C.37 | 0.000232 |
S | 980 | I980I | atC | atT | 2 | 2 | Q.2 | 0.001227 |
S | 980 | I980I | atC | atT | 1 | 2 | Q.3 | 0.000145 |
S | 980 | I980I | atC | atA | 1 | 2 | Q.3 | 0.000145 |
S | 980 | I980I | atC | atT | 2 | 2 | Q.6 | 0.013245 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.118 | 0.000063 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.29 | 0.000016 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.4.5 | 0.000107 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.45 | 0.000122 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.54 | 0.000095 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.6 | 0.000041 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.7.1 | 0.000113 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.74 | 0.000116 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.8 | 0.000606 |
S | 980 | I980I | atC | atT | 1 | 1 | AY.99.2 | 0.000092 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.214 | 0.000055 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.274 | 0.005051 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.318 | 0.000302 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.33 | 0.000421 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.389 | 0.006061 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.487 | 0.005587 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.507 | 0.008696 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.1.519 | 0.00004 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.119 | 0.010526 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.22 | 0.001318 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.221 | 0.000071 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.234 | 0.000132 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.340 | 0.004292 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.36.17 | 0.000494 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.36.8 | 0.001 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.370 | 0.008 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.441 | 0.009615 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.499 | 0.00105 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.525 | 0.000113 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.551 | 0.00129 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.561 | 0.000397 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.564 | 0.000426 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.571 | 0.009709 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.589 | 0.007576 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.617.1 | 0.000129 |
S | 980 | I980I | atC | atT | 1 | 1 | B.1.637 | 0.000073 |
S | 980 | I980I | atC | atT | 1 | 1 | B.12 | 0.00641 |
S | 980 | I980I | atC | atT | 1 | 1 | Q.7 | 0.001111 |
S | 980 | I980I | 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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