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 |
M | 108 | S108S | syn | tcC | tcT | 431 | 403 | 0.935035 | 26844-26846 | |
M | 108 | S108S | syn | tcC | tcA | 431 | 25 | 0.0580046 | 26844-26846 | |
M | 108 | S108S | syn | tcC | tcG | 431 | 2 | 0.00464037 | 26844-26846 | |
M | 108 | S108S | syn | TCc | AGc | 431 | 1 | 0.00232019 | 26844-26846 | |
M | 108 | S108del | del | TCC | --- | 91 | 91 | 1 | 26844-26846 | |
M | 108 | S108A | nonsyn | Tcc | Gcc | 12 | 12 | 1 | 26844-26846 | |
M | 108 | S108F | nonsyn | tCc | tTc | 9 | 7 | 0.777778 | 26844-26846 | |
M | 108 | S108F | nonsyn | tCC | tTT | 9 | 2 | 0.222222 | 26844-26846 | |
M | 108 | S108T | nonsyn | Tcc | Acc | 7 | 7 | 1 | 26844-26846 | |
M | 108 | S108P | nonsyn | Tcc | Ccc | 7 | 6 | 0.857143 | 26844-26846 | |
M | 108 | S108P | nonsyn | TcC | CcT | 7 | 1 | 0.142857 | 26844-26846 | |
M | 108 | S108C | nonsyn | tCc | tGc | 5 | 5 | 1 | 26844-26846 | |
M | 108 | S108Y | nonsyn | tCc | tAc | 5 | 5 | 1 | 26844-26846 | |
M | 108 | S108del2 | del | TCC | --G | 2 | 1 | 0.5 | 26844-26846 | |
M | 108 | S108del2 | del | TCc | --c | 2 | 1 | 0.5 | 26844-26846 | |
M | 108 | S108R | nonsyn | TCC | CGG | 1 | 1 | 1 | 26844-26846 | |
M | 108 | S108G | nonsyn | TCc | GGc | 1 | 1 | 1 | 26844-26846 | |
M | 108 | S108del1 | del | tCc | t-c | 1 | 1 | 1 | 26844-26846 |
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 |
M | 108 | S108S | tcC | tcT | 403 | 431 | All | 0.000077 |
M | 108 | S108S | tcC | tcA | 25 | 431 | All | 0.000005 |
M | 108 | S108S | tcC | tcG | 2 | 431 | All | 0 |
M | 108 | S108S | TCc | AGc | 1 | 431 | All | 0 |
M | 108 | S108del | TCC | --- | 91 | 91 | All | 0.000017 |
M | 108 | S108S | tcC | tcT | 84 | 84 | B.1.1.221 | 0.848485 |
M | 108 | S108del | TCC | --- | 75 | 75 | B.1.177.21 | 0.005735 |
M | 108 | S108S | tcC | tcT | 39 | 39 | AY.103 | 0.000242 |
M | 108 | S108S | tcC | tcT | 25 | 32 | B.1.1.7 | 0.000022 |
M | 108 | S108S | tcC | tcA | 7 | 32 | B.1.1.7 | 0.000006 |
M | 108 | S108S | tcC | tcT | 24 | 26 | AY.4 | 0.000037 |
M | 108 | S108S | tcC | tcG | 1 | 26 | AY.4 | 0.000002 |
M | 108 | S108S | tcC | tcA | 1 | 26 | AY.4 | 0.000002 |
M | 108 | S108S | tcC | tcT | 24 | 26 | B.1.617.2 | 0.00009 |
M | 108 | S108S | tcC | tcA | 2 | 26 | B.1.617.2 | 0.000008 |
M | 108 | S108S | tcC | tcT | 20 | 25 | AY.44 | 0.000122 |
M | 108 | S108S | tcC | tcA | 5 | 25 | AY.44 | 0.00003 |
M | 108 | S108S | tcC | tcT | 25 | 25 | B.1.2 | 0.00022 |
M | 108 | S108S | tcC | tcT | 21 | 21 | AY.25 | 0.000126 |
M | 108 | S108S | tcC | tcT | 15 | 15 | B.1.1.67 | 0.068493 |
M | 108 | S108S | tcC | tcT | 12 | 14 | B.1 | 0.00011 |
M | 108 | S108S | tcC | tcA | 2 | 14 | B.1 | 0.000018 |
M | 108 | S108A | Tcc | Gcc | 12 | 12 | All | 0.000002 |
M | 108 | S108S | tcC | tcT | 12 | 12 | P.1 | 0.000189 |
M | 108 | S108F | tCc | tTc | 7 | 9 | All | 0.000001 |
M | 108 | S108F | tCC | tTT | 2 | 9 | All | 0 |
M | 108 | S108del | TCC | --- | 9 | 9 | B.1.1.7 | 0.000008 |
M | 108 | S108S | tcC | tcT | 8 | 8 | B.1.177 | 0.000105 |
M | 108 | S108T | Tcc | Acc | 7 | 7 | All | 0.000001 |
M | 108 | S108P | Tcc | Ccc | 6 | 7 | All | 0.000001 |
M | 108 | S108P | TcC | CcT | 1 | 7 | All | 0 |
M | 108 | S108S | tcC | tcT | 7 | 7 | AY.12 | 0.002212 |
M | 108 | S108S | tcC | tcT | 5 | 6 | AY.43 | 0.000022 |
M | 108 | S108S | tcC | tcG | 1 | 6 | AY.43 | 0.000004 |
M | 108 | S108Y | tCc | tAc | 5 | 5 | All | 0.000001 |
M | 108 | S108C | tCc | tGc | 5 | 5 | All | 0.000001 |
M | 108 | S108S | tcC | tcT | 5 | 5 | AY.26 | 0.000142 |
M | 108 | S108S | tcC | tcT | 5 | 5 | AY.29 | 0.000079 |
M | 108 | S108S | tcC | tcT | 5 | 5 | P.1.2 | 0.00578 |
M | 108 | S108S | tcC | tcT | 4 | 4 | AY.24 | 0.001724 |
M | 108 | S108S | tcC | tcT | 4 | 4 | AY.75 | 0.000224 |
M | 108 | S108A | Tcc | Gcc | 4 | 4 | B.1.1.7 | 0.000004 |
M | 108 | S108S | tcC | tcT | 4 | 4 | P.2 | 0.000747 |
M | 108 | S108F | tCc | tTc | 2 | 3 | 0.111111 | |
M | 108 | S108F | tCC | tTT | 1 | 3 | 0.055556 | |
M | 108 | S108S | tcC | tcT | 3 | 3 | AY.5.4 | 0.00083 |
M | 108 | S108F | tCc | tTc | 2 | 3 | B.1 | 0.000018 |
M | 108 | S108F | tCC | tTT | 1 | 3 | B.1 | 0.000009 |
M | 108 | S108S | tcC | tcT | 3 | 3 | B.1.258 | 0.0002 |
M | 108 | S108S | tcC | tcT | 3 | 3 | B.1.525 | 0.000339 |
M | 108 | S108del2 | TCC | --G | 1 | 2 | All | 0 |
M | 108 | S108del2 | TCc | --c | 1 | 2 | All | 0 |
M | 108 | S108S | tcC | tcT | 1 | 2 | AY.102 | 0.000027 |
M | 108 | S108S | tcC | tcA | 1 | 2 | AY.102 | 0.000027 |
M | 108 | S108C | tCc | tGc | 2 | 2 | AY.103 | 0.000012 |
M | 108 | S108S | tcC | tcT | 2 | 2 | AY.116 | 0.000574 |
M | 108 | S108S | tcC | tcT | 1 | 2 | AY.3 | 0.00001 |
M | 108 | S108S | TCc | AGc | 1 | 2 | AY.3 | 0.00001 |
M | 108 | S108A | Tcc | Gcc | 2 | 2 | AY.43 | 0.000009 |
M | 108 | S108S | tcC | tcT | 2 | 2 | AY.5 | 0.000041 |
M | 108 | S108Y | tCc | tAc | 2 | 2 | B.1 | 0.000018 |
M | 108 | S108S | tcC | tcT | 2 | 2 | B.1.1.389 | 0.012121 |
M | 108 | S108S | tcC | tcT | 2 | 2 | B.1.179 | 0.007519 |
M | 108 | S108P | Tcc | Ccc | 2 | 2 | B.1.2 | 0.000018 |
M | 108 | S108T | Tcc | Acc | 2 | 2 | B.1.2 | 0.000018 |
M | 108 | S108S | tcC | tcA | 1 | 2 | B.1.221 | 0.000071 |
M | 108 | S108S | tcC | tcT | 1 | 2 | B.1.221 | 0.000071 |
M | 108 | S108S | tcC | tcT | 2 | 2 | B.1.258.17 | 0.000208 |
M | 108 | S108Y | tCc | tAc | 2 | 2 | B.1.617.2 | 0.000008 |
M | 108 | S108S | tcC | tcT | 2 | 2 | R.1 | 0.00018 |
M | 108 | S108S | tcC | tcT | 1 | 1 | 0.055556 | |
M | 108 | S108S | tcC | tcT | 1 | 1 | A | 0.000387 |
M | 108 | S108S | tcC | tcT | 1 | 1 | A.2.5 | 0.000499 |
M | 108 | S108R | TCC | CGG | 1 | 1 | All | 0 |
M | 108 | S108del1 | tCc | t-c | 1 | 1 | All | 0 |
M | 108 | S108G | TCc | GGc | 1 | 1 | All | 0 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.100 | 0.000046 |
M | 108 | S108R | TCC | CGG | 1 | 1 | AY.118 | 0.000063 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.119 | 0.000035 |
M | 108 | S108A | Tcc | Gcc | 1 | 1 | AY.120 | 0.000037 |
M | 108 | S108S | tcC | tcA | 1 | 1 | AY.120 | 0.000037 |
M | 108 | S108S | tcC | tcA | 1 | 1 | AY.120.1 | 0.000321 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.27 | 0.000065 |
M | 108 | S108del | TCC | --- | 1 | 1 | AY.3 | 0.00001 |
M | 108 | S108G | TCc | GGc | 1 | 1 | AY.3 | 0.00001 |
M | 108 | S108T | Tcc | Acc | 1 | 1 | AY.3 | 0.00001 |
M | 108 | S108A | Tcc | Gcc | 1 | 1 | AY.3 | 0.00001 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.4.2 | 0.000022 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.40 | 0.000964 |
M | 108 | S108T | Tcc | Acc | 1 | 1 | AY.43 | 0.000004 |
M | 108 | S108S | tcC | tcA | 1 | 1 | AY.46.2 | 0.000635 |
M | 108 | S108A | Tcc | Gcc | 1 | 1 | AY.46.6 | 0.000072 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.47 | 0.000031 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.55 | 0.000917 |
M | 108 | S108P | TcC | CcT | 1 | 1 | AY.60 | 0.000938 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.61 | 0.000105 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.64 | 0.000595 |
M | 108 | S108A | Tcc | Gcc | 1 | 1 | AY.67 | 0.000464 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.68 | 0.000274 |
M | 108 | S108S | tcC | tcA | 1 | 1 | AY.82 | 0.001357 |
M | 108 | S108S | tcC | tcT | 1 | 1 | AY.9 | 0.000068 |
M | 108 | S108del | TCC | --- | 1 | 1 | AY.9 | 0.000068 |
M | 108 | S108del2 | TCC | --G | 1 | 1 | AY.99 | 0.001049 |
M | 108 | S108del | TCC | --- | 1 | 1 | B.1 | 0.000009 |
M | 108 | S108P | Tcc | Ccc | 1 | 1 | B.1 | 0.000009 |
M | 108 | S108C | tCc | tGc | 1 | 1 | B.1.1 | 0.000018 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.1 | 0.000018 |
M | 108 | S108del | TCC | --- | 1 | 1 | B.1.1.221 | 0.010101 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.1.28 | 0.000311 |
M | 108 | S108S | tcC | tcA | 1 | 1 | B.1.1.311 | 0.000358 |
M | 108 | S108del | TCC | --- | 1 | 1 | B.1.1.372 | 0.000689 |
M | 108 | S108T | Tcc | Acc | 1 | 1 | B.1.1.404 | 0.015873 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.1.415 | 0.05 |
M | 108 | S108T | Tcc | Acc | 1 | 1 | B.1.1.7 | 0.000001 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.160 | 0.000031 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.177.28 | 0.007407 |
M | 108 | S108C | tCc | tGc | 1 | 1 | B.1.177.73 | 0.000566 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.177.8 | 0.000752 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.177.81 | 0.000189 |
M | 108 | S108Y | tCc | tAc | 1 | 1 | B.1.177.81 | 0.000189 |
M | 108 | S108A | Tcc | Gcc | 1 | 1 | B.1.177.86 | 0.000183 |
M | 108 | S108A | Tcc | Gcc | 1 | 1 | B.1.2 | 0.000009 |
M | 108 | S108del2 | TCc | --c | 1 | 1 | B.1.2 | 0.000009 |
M | 108 | S108F | tCc | tTc | 1 | 1 | B.1.2 | 0.000009 |
M | 108 | S108C | tCc | tGc | 1 | 1 | B.1.206 | 0.000816 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.234 | 0.000132 |
M | 108 | S108del | TCC | --- | 1 | 1 | B.1.258.11 | 0.000396 |
M | 108 | S108S | tcC | tcA | 1 | 1 | B.1.396 | 0.000706 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.438.1 | 0.000107 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.466.2 | 0.000391 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.513 | 0.013889 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.523 | 0.002451 |
M | 108 | S108T | Tcc | Acc | 1 | 1 | B.1.596 | 0.000087 |
M | 108 | S108F | tCc | tTc | 1 | 1 | B.1.596 | 0.000087 |
M | 108 | S108del | TCC | --- | 1 | 1 | B.1.617.1 | 0.000129 |
M | 108 | S108del1 | tCc | t-c | 1 | 1 | B.1.617.1 | 0.000129 |
M | 108 | S108F | tCc | tTc | 1 | 1 | B.1.617.2 | 0.000004 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.621 | 0.000089 |
M | 108 | S108P | Tcc | Ccc | 1 | 1 | B.1.632 | 0.006711 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.1.637 | 0.000073 |
M | 108 | S108P | Tcc | Ccc | 1 | 1 | B.15 | 0.017544 |
M | 108 | S108S | tcC | tcT | 1 | 1 | B.6 | 0.00091 |
M | 108 | S108S | tcC | tcT | 1 | 1 | C.36.3 | 0.000567 |
M | 108 | S108P | Tcc | Ccc | 1 | 1 | D.2 | 0.000075 |
M | 108 | S108S | tcC | tcT | 1 | 1 | P.1.15 | 0.000232 |
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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