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 |
E | 20 | F20L | nonsyn | ttT | ttG | 493 | 246 | 0.498986 | 26302-26304 | |
E | 20 | F20L | nonsyn | Ttt | Ctt | 493 | 236 | 0.478702 | 26302-26304 | |
E | 20 | F20L | nonsyn | ttT | ttA | 493 | 10 | 0.020284 | 26302-26304 | |
E | 20 | F20L | nonsyn | TtT | CtC | 493 | 1 | 0.0020284 | 26302-26304 | |
E | 20 | F20F | syn | ttT | ttC | 134 | 134 | 1 | 26302-26304 | |
E | 20 | F20I | nonsyn | Ttt | Att | 92 | 91 | 0.98913 | 26302-26304 | |
E | 20 | F20I | nonsyn | TtT | AtA | 92 | 1 | 0.0108696 | 26302-26304 | |
E | 20 | F20del | del | TTT | --- | 47 | 47 | 1 | 26302-26304 | |
E | 20 | F20S | nonsyn | tTt | tCt | 33 | 32 | 0.969697 | 26302-26304 | |
E | 20 | F20S | nonsyn | tTT | tCC | 33 | 1 | 0.030303 | 26302-26304 | |
E | 20 | F20del2 | del | tTT | t-- | 4 | 4 | 1 | 26302-26304 | |
E | 20 | F20del1 | del | ttT | tt- | 4 | 3 | 0.75 | 26302-26304 | |
E | 20 | F20del1 | del | TtT | Nt- | 4 | 1 | 0.25 | 26302-26304 | |
E | 20 | F20V | nonsyn | Ttt | Gtt | 3 | 3 | 1 | 26302-26304 | |
E | 20 | F20Y | nonsyn | tTT | tAC | 2 | 1 | 0.5 | 26302-26304 | |
E | 20 | F20Y | nonsyn | tTt | tAt | 2 | 1 | 0.5 | 26302-26304 | |
E | 20 | F20P | nonsyn | TTT | CCC | 2 | 1 | 0.5 | 26302-26304 | |
E | 20 | F20P | nonsyn | TTt | CCt | 2 | 1 | 0.5 | 26302-26304 | |
E | 20 | F20C | nonsyn | tTt | tGt | 1 | 1 | 1 | 26302-26304 | |
E | 20 | F20N | nonsyn | TTT | AAC | 1 | 1 | 1 | 26302-26304 |
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 |
E | 20 | F20L | ttT | ttG | 246 | 493 | All | 0.000047 |
E | 20 | F20L | Ttt | Ctt | 236 | 493 | All | 0.000045 |
E | 20 | F20L | ttT | ttA | 10 | 493 | All | 0.000002 |
E | 20 | F20L | TtT | CtC | 1 | 493 | All | 0 |
E | 20 | F20L | ttT | ttG | 192 | 192 | AY.70 | 0.040033 |
E | 20 | F20F | ttT | ttC | 134 | 134 | All | 0.000026 |
E | 20 | F20L | Ttt | Ctt | 124 | 124 | B.1.177.4 | 0.026171 |
E | 20 | F20I | Ttt | Att | 91 | 92 | All | 0.000017 |
E | 20 | F20I | TtT | AtA | 1 | 92 | All | 0 |
E | 20 | F20del | TTT | --- | 47 | 47 | All | 0.000009 |
E | 20 | F20L | ttT | ttG | 41 | 41 | B.1.616 | 1 |
E | 20 | F20S | tTt | tCt | 32 | 33 | All | 0.000006 |
E | 20 | F20S | tTT | tCC | 1 | 33 | All | 0 |
E | 20 | F20L | Ttt | Ctt | 29 | 29 | B.1.177.60 | 0.006335 |
E | 20 | F20F | ttT | ttC | 20 | 20 | AY.36 | 0.002964 |
E | 20 | F20I | Ttt | Att | 16 | 16 | AY.36 | 0.002371 |
E | 20 | F20F | ttT | ttC | 16 | 16 | B.1.243 | 0.001113 |
E | 20 | F20F | ttT | ttC | 15 | 15 | AY.4 | 0.000023 |
E | 20 | F20L | Ttt | Ctt | 9 | 15 | B.1.1.7 | 0.000008 |
E | 20 | F20L | ttT | ttG | 6 | 15 | B.1.1.7 | 0.000005 |
E | 20 | F20I | Ttt | Att | 14 | 14 | B.1.1.7 | 0.000013 |
E | 20 | F20I | Ttt | Att | 13 | 13 | A.1 | 0.003664 |
E | 20 | F20L | Ttt | Ctt | 11 | 11 | AY.39 | 0.000272 |
E | 20 | F20L | ttT | ttA | 9 | 11 | B.1.177 | 0.000119 |
E | 20 | F20L | Ttt | Ctt | 2 | 11 | B.1.177 | 0.000026 |
E | 20 | F20I | Ttt | Att | 10 | 10 | AY.44 | 0.000061 |
E | 20 | F20S | tTt | tCt | 8 | 8 | B.1.1.7 | 0.000007 |
E | 20 | F20F | ttT | ttC | 8 | 8 | B.1.1.7 | 0.000007 |
E | 20 | F20F | ttT | ttC | 8 | 8 | B.1.234 | 0.001056 |
E | 20 | F20F | ttT | ttC | 7 | 7 | B.1.177.11 | 0.011885 |
E | 20 | F20I | Ttt | Att | 7 | 7 | B.1.36.18 | 0.002941 |
E | 20 | F20L | Ttt | Ctt | 6 | 6 | AY.25 | 0.000036 |
E | 20 | F20del | TTT | --- | 6 | 6 | B | 0.000767 |
E | 20 | F20L | Ttt | Ctt | 6 | 6 | B.1.617.2 | 0.000023 |
E | 20 | F20I | Ttt | Att | 6 | 6 | R.1 | 0.00054 |
E | 20 | F20I | Ttt | Att | 5 | 5 | AY.43 | 0.000022 |
E | 20 | F20L | Ttt | Ctt | 4 | 5 | AY.59 | 0.002119 |
E | 20 | F20L | ttT | ttG | 1 | 5 | AY.59 | 0.00053 |
E | 20 | F20L | Ttt | Ctt | 5 | 5 | B.1.1 | 0.000091 |
E | 20 | F20L | Ttt | Ctt | 5 | 5 | B.1.1.519 | 0.000199 |
E | 20 | F20del | TTT | --- | 5 | 5 | P.1 | 0.000079 |
E | 20 | F20del | TTT | --- | 5 | 5 | P.1.15 | 0.001162 |
E | 20 | F20del2 | tTT | t-- | 4 | 4 | All | 0.000001 |
E | 20 | F20del1 | ttT | tt- | 3 | 4 | All | 0.000001 |
E | 20 | F20del1 | TtT | Nt- | 1 | 4 | All | 0 |
E | 20 | F20F | ttT | ttC | 4 | 4 | AY.103 | 0.000025 |
E | 20 | F20L | Ttt | Ctt | 2 | 4 | AY.103 | 0.000012 |
E | 20 | F20L | ttT | ttA | 1 | 4 | AY.103 | 0.000006 |
E | 20 | F20L | ttT | ttG | 1 | 4 | AY.103 | 0.000006 |
E | 20 | F20F | ttT | ttC | 4 | 4 | AY.44 | 0.000024 |
E | 20 | F20L | Ttt | Ctt | 4 | 4 | B.1 | 0.000037 |
E | 20 | F20F | ttT | ttC | 4 | 4 | B.1.351 | 0.000119 |
E | 20 | F20I | Ttt | Att | 4 | 4 | B.1.429 | 0.000094 |
E | 20 | F20F | ttT | ttC | 3 | 3 | 0.166667 | |
E | 20 | F20V | Ttt | Gtt | 3 | 3 | All | 0.000001 |
E | 20 | F20S | tTt | tCt | 3 | 3 | AY.102 | 0.00008 |
E | 20 | F20L | Ttt | Ctt | 3 | 3 | AY.43 | 0.000013 |
E | 20 | F20F | ttT | ttC | 3 | 3 | AY.43 | 0.000013 |
E | 20 | F20del | TTT | --- | 3 | 3 | AY.43 | 0.000013 |
E | 20 | F20F | ttT | ttC | 3 | 3 | AY.6 | 0.000123 |
E | 20 | F20S | tTt | tCt | 3 | 3 | B.1 | 0.000027 |
E | 20 | F20del | TTT | --- | 3 | 3 | B.1.1.7 | 0.000003 |
E | 20 | F20F | ttT | ttC | 3 | 3 | B.1.2 | 0.000026 |
E | 20 | F20I | Ttt | Att | 3 | 3 | B.1.617.2 | 0.000011 |
E | 20 | F20F | ttT | ttC | 3 | 3 | P.1.7 | 0.000958 |
E | 20 | F20S | tTt | tCt | 1 | 2 | 0.055556 | |
E | 20 | F20L | Ttt | Ctt | 1 | 2 | 0.055556 | |
E | 20 | F20S | tTT | tCC | 1 | 2 | 0.055556 | |
E | 20 | F20L | TtT | CtC | 1 | 2 | 0.055556 | |
E | 20 | F20P | TTT | CCC | 1 | 2 | 0.055556 | |
E | 20 | F20P | TTt | CCt | 1 | 2 | 0.055556 | |
E | 20 | F20P | TTt | CCt | 1 | 2 | All | 0 |
E | 20 | F20P | TTT | CCC | 1 | 2 | All | 0 |
E | 20 | F20Y | tTT | tAC | 1 | 2 | All | 0 |
E | 20 | F20Y | tTt | tAt | 1 | 2 | All | 0 |
E | 20 | F20F | ttT | ttC | 2 | 2 | AY.102 | 0.000053 |
E | 20 | F20L | Ttt | Ctt | 2 | 2 | AY.102 | 0.000053 |
E | 20 | F20F | ttT | ttC | 2 | 2 | AY.113 | 0.000285 |
E | 20 | F20S | tTt | tCt | 2 | 2 | AY.117 | 0.000169 |
E | 20 | F20del | TTT | --- | 2 | 2 | AY.26 | 0.000057 |
E | 20 | F20L | Ttt | Ctt | 2 | 2 | AY.29 | 0.000032 |
E | 20 | F20F | ttT | ttC | 2 | 2 | AY.29.1 | 0.000441 |
E | 20 | F20L | Ttt | Ctt | 2 | 2 | AY.4.2.1 | 0.000298 |
E | 20 | F20F | ttT | ttC | 2 | 2 | AY.9.2 | 0.000073 |
E | 20 | F20I | Ttt | Att | 2 | 2 | AZ.2 | 0.001642 |
E | 20 | F20del | TTT | --- | 2 | 2 | B.1 | 0.000018 |
E | 20 | F20del1 | ttT | tt- | 1 | 2 | B.1 | 0.000009 |
E | 20 | F20del1 | TtT | Nt- | 1 | 2 | B.1 | 0.000009 |
E | 20 | F20S | tTt | tCt | 2 | 2 | B.1.1 | 0.000036 |
E | 20 | F20F | ttT | ttC | 2 | 2 | B.1.177.56 | 0.001335 |
E | 20 | F20L | Ttt | Ctt | 2 | 2 | B.1.2 | 0.000018 |
E | 20 | F20F | ttT | ttC | 2 | 2 | B.1.243.1 | 0.044444 |
E | 20 | F20S | tTt | tCt | 2 | 2 | B.1.258.11 | 0.000793 |
E | 20 | F20F | ttT | ttC | 2 | 2 | B.1.525 | 0.000226 |
E | 20 | F20L | Ttt | Ctt | 1 | 2 | B.1.526 | 0.000024 |
E | 20 | F20L | ttT | ttG | 1 | 2 | B.1.526 | 0.000024 |
E | 20 | F20F | ttT | ttC | 2 | 2 | B.1.617.2 | 0.000008 |
E | 20 | F20del2 | tTT | t-- | 2 | 2 | B.1.621 | 0.000177 |
E | 20 | F20del | TTT | --- | 2 | 2 | C.37 | 0.000232 |
E | 20 | F20del | TTT | --- | 2 | 2 | C.37.1 | 0.005236 |
E | 20 | F20N | TTT | AAC | 1 | 1 | All | 0 |
E | 20 | F20C | tTt | tGt | 1 | 1 | All | 0 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.10 | 0.00053 |
E | 20 | F20I | Ttt | Att | 1 | 1 | AY.100 | 0.000046 |
E | 20 | F20F | ttT | ttC | 1 | 1 | AY.118 | 0.000063 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.118 | 0.000063 |
E | 20 | F20F | ttT | ttC | 1 | 1 | AY.121 | 0.000135 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.25 | 0.000006 |
E | 20 | F20del2 | tTT | t-- | 1 | 1 | AY.25 | 0.000006 |
E | 20 | F20I | Ttt | Att | 1 | 1 | AY.25 | 0.000006 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.3 | 0.00001 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | AY.3 | 0.00001 |
E | 20 | F20L | ttT | ttG | 1 | 1 | AY.33 | 0.000067 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.39 | 0.000025 |
E | 20 | F20del2 | tTT | t-- | 1 | 1 | AY.39 | 0.000025 |
E | 20 | F20V | Ttt | Gtt | 1 | 1 | AY.4 | 0.000002 |
E | 20 | F20I | Ttt | Att | 1 | 1 | AY.4 | 0.000002 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | AY.4 | 0.000002 |
E | 20 | F20Y | tTt | tAt | 1 | 1 | AY.4 | 0.000002 |
E | 20 | F20F | ttT | ttC | 1 | 1 | AY.4.2.1 | 0.000149 |
E | 20 | F20S | tTt | tCt | 1 | 1 | AY.42 | 0.00004 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | AY.44 | 0.000006 |
E | 20 | F20I | Ttt | Att | 1 | 1 | AY.46.4 | 0.000165 |
E | 20 | F20F | ttT | ttC | 1 | 1 | AY.5 | 0.000021 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | AY.5 | 0.000021 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.54 | 0.000095 |
E | 20 | F20I | Ttt | Att | 1 | 1 | AY.55 | 0.000917 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | AY.61 | 0.000105 |
E | 20 | F20F | ttT | ttC | 1 | 1 | AY.61 | 0.000105 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.68 | 0.000274 |
E | 20 | F20del | TTT | --- | 1 | 1 | AY.75 | 0.000056 |
E | 20 | F20I | Ttt | Att | 1 | 1 | AY.78 | 0.001541 |
E | 20 | F20N | TTT | AAC | 1 | 1 | AY.85 | 0.000427 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | AY.9 | 0.000068 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B | 0.000128 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1 | 0.000009 |
E | 20 | F20C | tTt | tGt | 1 | 1 | B.1 | 0.000009 |
E | 20 | F20V | Ttt | Gtt | 1 | 1 | B.1 | 0.000009 |
E | 20 | F20I | Ttt | Att | 1 | 1 | B.1 | 0.000009 |
E | 20 | F20del | TTT | --- | 1 | 1 | B.1.1 | 0.000018 |
E | 20 | F20S | tTt | tCt | 1 | 1 | B.1.1.135 | 0.004695 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.1.25 | 0.000569 |
E | 20 | F20Y | tTT | tAC | 1 | 1 | B.1.1.306 | 0.000438 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.1.317 | 0.000412 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1.1.409 | 0.002833 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.1.433 | 0.001425 |
E | 20 | F20del | TTT | --- | 1 | 1 | B.1.1.8 | 0.003584 |
E | 20 | F20V | Ttt | Gtt | 1 | 1 | B.1.160 | 0.000031 |
E | 20 | F20del | TTT | --- | 1 | 1 | B.1.177 | 0.000013 |
E | 20 | F20S | tTt | tCt | 1 | 1 | B.1.177 | 0.000013 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1.177.57 | 0.000281 |
E | 20 | F20S | tTt | tCt | 1 | 1 | B.1.2 | 0.000009 |
E | 20 | F20I | TtT | AtA | 1 | 1 | B.1.210 | 0.002132 |
E | 20 | F20del | TTT | --- | 1 | 1 | B.1.218 | 0.005155 |
E | 20 | F20L | ttT | ttG | 1 | 1 | B.1.221 | 0.000071 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.23 | 0.006061 |
E | 20 | F20I | Ttt | Att | 1 | 1 | B.1.234 | 0.000132 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1.236 | 0.002053 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.243 | 0.00007 |
E | 20 | F20del | TTT | --- | 1 | 1 | B.1.258 | 0.000067 |
E | 20 | F20S | tTt | tCt | 1 | 1 | B.1.258 | 0.000067 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.337 | 0.005587 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.36 | 0.000146 |
E | 20 | F20I | Ttt | Att | 1 | 1 | B.1.36.10 | 0.004785 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1.360 | 0.012658 |
E | 20 | F20S | tTt | tCt | 1 | 1 | B.1.429 | 0.000024 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1.466.2 | 0.000391 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.515 | 0.014493 |
E | 20 | F20del1 | ttT | tt- | 1 | 1 | B.1.525 | 0.000113 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | B.1.527 | 0.003704 |
E | 20 | F20L | ttT | ttG | 1 | 1 | B.1.576 | 0.000907 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1.582 | 0.000491 |
E | 20 | F20S | tTt | tCt | 1 | 1 | B.1.617.2 | 0.000004 |
E | 20 | F20del1 | ttT | tt- | 1 | 1 | B.1.621 | 0.000089 |
E | 20 | F20del | TTT | --- | 1 | 1 | B.1.621 | 0.000089 |
E | 20 | F20I | Ttt | Att | 1 | 1 | B.1.621 | 0.000089 |
E | 20 | F20I | Ttt | Att | 1 | 1 | B.1.625 | 0.002353 |
E | 20 | F20F | ttT | ttC | 1 | 1 | B.1.626 | 0.005714 |
E | 20 | F20del | TTT | --- | 1 | 1 | B.1.627 | 0.00202 |
E | 20 | F20S | tTt | tCt | 1 | 1 | B.1.637 | 0.000073 |
E | 20 | F20S | tTt | tCt | 1 | 1 | D.2 | 0.000075 |
E | 20 | F20F | ttT | ttC | 1 | 1 | P.1 | 0.000016 |
E | 20 | F20S | tTt | tCt | 1 | 1 | P.1 | 0.000016 |
E | 20 | F20L | ttT | ttG | 1 | 1 | P.1 | 0.000016 |
E | 20 | F20del | TTT | --- | 1 | 1 | P.1.13 | 0.000898 |
E | 20 | F20F | ttT | ttC | 1 | 1 | P.1.14 | 0.000048 |
E | 20 | F20L | Ttt | Ctt | 1 | 1 | P.1.15 | 0.000232 |
E | 20 | F20del | TTT | --- | 1 | 1 | P.1.7 | 0.000319 |
E | 20 | F20S | tTt | tCt | 1 | 1 | P.2 | 0.000187 |
E | 20 | F20F | ttT | ttC | 1 | 1 | Q.2 | 0.000613 |
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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