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/nsp3 | 1608 | I1608I | I2426I | syn | atT | atC | 1535 | 1521 | 0.990879 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608I | I2426I | syn | atT | atA | 1535 | 14 | 0.00912052 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608del | I2426del | del | ATT | --- | 84 | 84 | 1 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608V | I2426V | nonsyn | Att | Gtt | 15 | 13 | 0.866667 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608V | I2426V | nonsyn | AtT | GtA | 15 | 2 | 0.133333 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608F | I2426F | nonsyn | Att | Ttt | 11 | 10 | 0.909091 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608L | I2426L | nonsyn | Att | Ctt | 11 | 9 | 0.818182 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608L | I2426L | nonsyn | AtT | TtA | 11 | 2 | 0.181818 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608F | I2426F | nonsyn | AtT | TtC | 11 | 1 | 0.0909091 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608del1 | I2426del1 | del | Att | -tt | 7 | 4 | 0.571429 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608del1 | I2426del1 | del | atT | at- | 7 | 2 | 0.285714 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608del1 | I2426del1 | del | aTt | a-t | 7 | 1 | 0.142857 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608M | I2426M | nonsyn | atT | atG | 4 | 4 | 1 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608T | I2426T | nonsyn | aTt | aCt | 4 | 3 | 0.75 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608T | I2426T | nonsyn | aTT | aCG | 4 | 1 | 0.25 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608X | I2426X | nonsyn | ATT | TAA | 2 | 2 | 1 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608E | I2426E | nonsyn | ATT | GAA | 2 | 2 | 1 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608C | I2426C | nonsyn | ATt | TGt | 1 | 1 | 1 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608del2 | I2426del2 | del | aTT | a-- | 1 | 1 | 1 | 7541-7543 |
ORF1ab/nsp3 | 1608 | I1608N | I2426N | nonsyn | aTt | aAt | 1 | 1 | 1 | 7541-7543 |
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/nsp3 | 1608 | I1608I | atT | atC | 1521 | 1535 | All | 0.000291 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 14 | 1535 | All | 0.000003 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1252 | 1252 | B.1.177.73 | 0.708947 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 107 | 107 | B.1.177 | 0.001409 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 84 | 84 | All | 0.000016 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 70 | 70 | AY.4 | 0.000109 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 35 | 35 | B.1.1.7 | 0.000031 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 29 | 29 | AY.46 | 0.003018 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 16 | 16 | AY.96 | 0.033195 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 13 | 15 | All | 0.000002 |
ORF1ab/nsp3 | 1608 | I1608V | AtT | GtA | 2 | 15 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 13 | 14 | AY.3 | 0.000129 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 1 | 14 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 10 | 11 | All | 0.000002 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 9 | 11 | All | 0.000002 |
ORF1ab/nsp3 | 1608 | I1608L | AtT | TtA | 2 | 11 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608F | AtT | TtC | 1 | 11 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 8 | 8 | B.1.177 | 0.000105 |
ORF1ab/nsp3 | 1608 | I1608del1 | Att | -tt | 4 | 7 | All | 0.000001 |
ORF1ab/nsp3 | 1608 | I1608del1 | atT | at- | 2 | 7 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608del1 | aTt | a-t | 1 | 7 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 4 | 7 | B.1.1.7 | 0.000004 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 3 | 7 | B.1.1.7 | 0.000003 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 5 | 5 | AY.4 | 0.000008 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 5 | 5 | B.1 | 0.000046 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 5 | 5 | B.1.617.2 | 0.000019 |
ORF1ab/nsp3 | 1608 | I1608M | atT | atG | 4 | 4 | All | 0.000001 |
ORF1ab/nsp3 | 1608 | I1608T | aTt | aCt | 3 | 4 | All | 0.000001 |
ORF1ab/nsp3 | 1608 | I1608T | aTT | aCG | 1 | 4 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 4 | 4 | AY.103 | 0.000025 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 4 | 4 | B.1.499 | 0.004202 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 3 | 3 | AY.103 | 0.000019 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 3 | 3 | B.1.1.7 | 0.000003 |
ORF1ab/nsp3 | 1608 | I1608del1 | Att | -tt | 2 | 3 | B.1.2 | 0.000018 |
ORF1ab/nsp3 | 1608 | I1608del1 | atT | at- | 1 | 3 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608L | AtT | TtA | 2 | 2 | 0.111111 | |
ORF1ab/nsp3 | 1608 | I1608V | AtT | GtA | 2 | 2 | 0.111111 | |
ORF1ab/nsp3 | 1608 | I1608X | ATT | TAA | 2 | 2 | 0.111111 | |
ORF1ab/nsp3 | 1608 | I1608E | ATT | GAA | 2 | 2 | 0.111111 | |
ORF1ab/nsp3 | 1608 | I1608E | ATT | GAA | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608X | ATT | TAA | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 2 | 2 | AY.120 | 0.000074 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 2 | 2 | AY.29 | 0.000032 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 2 | 2 | AY.3 | 0.00002 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 2 | 2 | AY.43 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 2 | 2 | B.1.1 | 0.000036 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 2 | 2 | B.1.160.20 | 0.017857 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 2 | 2 | B.1.177.16 | 0.001329 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 2 | 2 | B.1.177.54 | 0.001213 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 2 | 2 | R.1 | 0.00018 |
ORF1ab/nsp3 | 1608 | I1608N | aTt | aAt | 1 | 1 | 0.055556 | |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | A | 0.000387 |
ORF1ab/nsp3 | 1608 | I1608C | ATt | TGt | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608N | aTt | aAt | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608del2 | aTT | a-- | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | AY.101 | 0.00049 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 1 | 1 | AY.114 | 0.000231 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | AY.24 | 0.000431 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 1608 | I1608C | ATt | TGt | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | AY.32 | 0.000532 |
ORF1ab/nsp3 | 1608 | I1608M | atT | atG | 1 | 1 | AY.33 | 0.000067 |
ORF1ab/nsp3 | 1608 | I1608M | atT | atG | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 1608 | I1608del1 | Att | -tt | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp3 | 1608 | I1608del1 | Att | -tt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | AY.46.2 | 0.000635 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | AY.6 | 0.000041 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | AY.66 | 0.00107 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 1 | 1 | AY.74 | 0.000116 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | AY.82 | 0.001357 |
ORF1ab/nsp3 | 1608 | I1608T | aTt | aCt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.1.159 | 0.004673 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.1.232 | 0.001815 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.1.236 | 0.006897 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.1.315 | 0.008475 |
ORF1ab/nsp3 | 1608 | I1608M | atT | atG | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.1.46 | 0.004367 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 1 | 1 | B.1.1.58 | 0.005376 |
ORF1ab/nsp3 | 1608 | I1608del1 | atT | at- | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1608 | I1608M | atT | atG | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1608 | I1608F | AtT | TtC | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1608 | I1608del2 | aTT | a-- | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.161 | 0.017241 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.177.19 | 0.001431 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.177.21 | 0.000076 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.177.51 | 0.004566 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.177.57 | 0.000281 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.177.81 | 0.000189 |
ORF1ab/nsp3 | 1608 | I1608T | aTT | aCG | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608V | Att | Gtt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | B.1.221 | 0.000071 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 1 | 1 | B.1.243 | 0.00007 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 1 | 1 | B.1.36.16 | 0.001425 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | B.1.408 | 0.00369 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp3 | 1608 | I1608L | Att | Ctt | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 1608 | I1608del1 | aTt | a-t | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | B.1.605 | 0.005952 |
ORF1ab/nsp3 | 1608 | I1608F | Att | Ttt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 1608 | I1608T | aTt | aCt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atC | 1 | 1 | B.1.619 | 0.000871 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | B.1.621 | 0.000089 |
ORF1ab/nsp3 | 1608 | I1608T | aTt | aCt | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp3 | 1608 | I1608I | atT | atA | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp3 | 1608 | I1608del | ATT | --- | 1 | 1 | U.3 | 0.003861 |
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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