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 |
ORF3a | 160 | Y160Y | syn | taC | taT | 20691 | 20691 | 1 | 25870-25872 | |
ORF3a | 160 | Y160H | nonsyn | Tac | Cac | 162 | 162 | 1 | 25870-25872 | |
ORF3a | 160 | Y160del | del | TAC | --- | 67 | 67 | 1 | 25870-25872 | |
ORF3a | 160 | Y160C | nonsyn | tAc | tGc | 51 | 51 | 1 | 25870-25872 | |
ORF3a | 160 | Y160X | nonsyn | taC | taA | 8 | 7 | 0.875 | 25870-25872 | |
ORF3a | 160 | Y160X | nonsyn | taC | taG | 8 | 1 | 0.125 | 25870-25872 | |
ORF3a | 160 | Y160S | nonsyn | tAc | tCc | 5 | 3 | 0.6 | 25870-25872 | |
ORF3a | 160 | Y160S | nonsyn | tAC | tCA | 5 | 2 | 0.4 | 25870-25872 | |
ORF3a | 160 | Y160F | nonsyn | tAc | tTc | 4 | 4 | 1 | 25870-25872 | |
ORF3a | 160 | Y160A | nonsyn | TAC | GCA | 4 | 2 | 0.5 | 25870-25872 | |
ORF3a | 160 | Y160A | nonsyn | TAc | GCc | 4 | 2 | 0.5 | 25870-25872 | |
ORF3a | 160 | Y160N | nonsyn | Tac | Aac | 2 | 2 | 1 | 25870-25872 | |
ORF3a | 160 | Y160D | nonsyn | Tac | Gac | 2 | 2 | 1 | 25870-25872 | |
ORF3a | 160 | Y160E | nonsyn | TaC | GaA | 2 | 2 | 1 | 25870-25872 | |
ORF3a | 160 | Y160del1 | del | tAc | t-c | 1 | 1 | 1 | 25870-25872 |
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 |
ORF3a | 160 | Y160Y | taC | taT | 20691 | 20691 | All | 0.003957 |
ORF3a | 160 | Y160Y | taC | taT | 20282 | 20282 | AY.42 | 0.815947 |
ORF3a | 160 | Y160H | Tac | Cac | 162 | 162 | All | 0.000031 |
ORF3a | 160 | Y160H | Tac | Cac | 87 | 87 | AY.4.2 | 0.001887 |
ORF3a | 160 | Y160Y | taC | taT | 79 | 79 | B.1.617.2 | 0.000297 |
ORF3a | 160 | Y160del | TAC | --- | 67 | 67 | All | 0.000013 |
ORF3a | 160 | Y160Y | taC | taT | 62 | 62 | P.1 | 0.000977 |
ORF3a | 160 | Y160Y | taC | taT | 60 | 60 | AY.3 | 0.000597 |
ORF3a | 160 | Y160C | tAc | tGc | 51 | 51 | All | 0.00001 |
ORF3a | 160 | Y160C | tAc | tGc | 35 | 35 | AY.43 | 0.000155 |
ORF3a | 160 | Y160H | Tac | Cac | 34 | 34 | B.1.1.7 | 0.00003 |
ORF3a | 160 | Y160Y | taC | taT | 27 | 27 | B.1.205 | 0.642857 |
ORF3a | 160 | Y160Y | taC | taT | 19 | 19 | AY.4 | 0.00003 |
ORF3a | 160 | Y160Y | taC | taT | 19 | 19 | AY.44 | 0.000116 |
ORF3a | 160 | Y160del | TAC | --- | 19 | 19 | B.1.1.7 | 0.000017 |
ORF3a | 160 | Y160Y | taC | taT | 16 | 16 | AY.43 | 0.000071 |
ORF3a | 160 | Y160H | Tac | Cac | 13 | 13 | AY.4 | 0.00002 |
ORF3a | 160 | Y160Y | taC | taT | 12 | 12 | AY.25 | 0.000072 |
ORF3a | 160 | Y160Y | taC | taT | 11 | 11 | B.1.1.7 | 0.00001 |
ORF3a | 160 | Y160X | taC | taA | 7 | 8 | All | 0.000001 |
ORF3a | 160 | Y160X | taC | taG | 1 | 8 | All | 0 |
ORF3a | 160 | Y160Y | taC | taT | 8 | 8 | B.1 | 0.000073 |
ORF3a | 160 | Y160Y | taC | taT | 6 | 6 | AY.99.2 | 0.000553 |
ORF3a | 160 | Y160del | TAC | --- | 6 | 6 | B.1 | 0.000055 |
ORF3a | 160 | Y160Y | taC | taT | 6 | 6 | B.1.517 | 0.002562 |
ORF3a | 160 | Y160S | tAc | tCc | 3 | 5 | All | 0.000001 |
ORF3a | 160 | Y160S | tAC | tCA | 2 | 5 | All | 0 |
ORF3a | 160 | Y160Y | taC | taT | 5 | 5 | AY.113 | 0.000712 |
ORF3a | 160 | Y160Y | taC | taT | 5 | 5 | AY.20 | 0.000194 |
ORF3a | 160 | Y160S | tAc | tCc | 2 | 4 | 0.111111 | |
ORF3a | 160 | Y160S | tAC | tCA | 2 | 4 | 0.111111 | |
ORF3a | 160 | Y160A | TAc | GCc | 2 | 4 | 0.111111 | |
ORF3a | 160 | Y160A | TAC | GCA | 2 | 4 | 0.111111 | |
ORF3a | 160 | Y160F | tAc | tTc | 4 | 4 | All | 0.000001 |
ORF3a | 160 | Y160A | TAc | GCc | 2 | 4 | All | 0 |
ORF3a | 160 | Y160A | TAC | GCA | 2 | 4 | All | 0 |
ORF3a | 160 | Y160Y | taC | taT | 4 | 4 | AY.102 | 0.000106 |
ORF3a | 160 | Y160Y | taC | taT | 4 | 4 | AY.26 | 0.000113 |
ORF3a | 160 | Y160C | tAc | tGc | 4 | 4 | AY.4 | 0.000006 |
ORF3a | 160 | Y160Y | taC | taT | 4 | 4 | AY.9.2 | 0.000147 |
ORF3a | 160 | Y160H | Tac | Cac | 4 | 4 | B.1 | 0.000037 |
ORF3a | 160 | Y160Y | taC | taT | 3 | 3 | AY.117 | 0.000254 |
ORF3a | 160 | Y160Y | taC | taT | 3 | 3 | AY.39 | 0.000074 |
ORF3a | 160 | Y160del | TAC | --- | 3 | 3 | AY.43 | 0.000013 |
ORF3a | 160 | Y160C | tAc | tGc | 3 | 3 | AY.44 | 0.000018 |
ORF3a | 160 | Y160Y | taC | taT | 3 | 3 | AY.98.1 | 0.000145 |
ORF3a | 160 | Y160Y | taC | taT | 3 | 3 | B.1.1.222 | 0.000612 |
ORF3a | 160 | Y160del | TAC | --- | 3 | 3 | B.1.177 | 0.00004 |
ORF3a | 160 | Y160E | TaC | GaA | 2 | 2 | 0.111111 | |
ORF3a | 160 | Y160X | taC | taA | 2 | 2 | 0.111111 | |
ORF3a | 160 | Y160del | TAC | --- | 2 | 2 | 0.111111 | |
ORF3a | 160 | Y160D | Tac | Gac | 2 | 2 | 0.111111 | |
ORF3a | 160 | Y160N | Tac | Aac | 2 | 2 | All | 0 |
ORF3a | 160 | Y160D | Tac | Gac | 2 | 2 | All | 0 |
ORF3a | 160 | Y160E | TaC | GaA | 2 | 2 | All | 0 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | AY.23 | 0.000139 |
ORF3a | 160 | Y160H | Tac | Cac | 2 | 2 | AY.3 | 0.00002 |
ORF3a | 160 | Y160F | tAc | tTc | 2 | 2 | AY.3 | 0.00002 |
ORF3a | 160 | Y160H | Tac | Cac | 2 | 2 | AY.39 | 0.000049 |
ORF3a | 160 | Y160del | TAC | --- | 2 | 2 | AY.4 | 0.000003 |
ORF3a | 160 | Y160X | taC | taA | 1 | 2 | AY.4 | 0.000002 |
ORF3a | 160 | Y160X | taC | taG | 1 | 2 | AY.4 | 0.000002 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | AY.4.1 | 0.001475 |
ORF3a | 160 | Y160H | Tac | Cac | 2 | 2 | AY.43 | 0.000009 |
ORF3a | 160 | Y160H | Tac | Cac | 2 | 2 | AY.45 | 0.000243 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | AY.46 | 0.000208 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | AY.46.6 | 0.000144 |
ORF3a | 160 | Y160H | Tac | Cac | 2 | 2 | AY.5 | 0.000041 |
ORF3a | 160 | Y160C | tAc | tGc | 2 | 2 | AY.74 | 0.000231 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | AY.75 | 0.000112 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | AY.92 | 0.000575 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | AY.98 | 0.000158 |
ORF3a | 160 | Y160C | tAc | tGc | 2 | 2 | AY.98.1 | 0.000097 |
ORF3a | 160 | Y160del | TAC | --- | 2 | 2 | B.1.1.315 | 0.016949 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | B.1.177.81 | 0.000379 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | B.1.2 | 0.000018 |
ORF3a | 160 | Y160H | Tac | Cac | 2 | 2 | B.1.427 | 0.000101 |
ORF3a | 160 | Y160del | TAC | --- | 2 | 2 | B.1.617.2 | 0.000008 |
ORF3a | 160 | Y160del | TAC | --- | 2 | 2 | B.1.621 | 0.000177 |
ORF3a | 160 | Y160H | Tac | Cac | 2 | 2 | P.1 | 0.000032 |
ORF3a | 160 | Y160del | TAC | --- | 2 | 2 | P.1 | 0.000032 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | P.1.12 | 0.000968 |
ORF3a | 160 | Y160del | TAC | --- | 2 | 2 | P.1.15 | 0.000465 |
ORF3a | 160 | Y160Y | taC | taT | 2 | 2 | P.1.7 | 0.000639 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | A | 0.000387 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | AD.2 | 0.000219 |
ORF3a | 160 | Y160del1 | tAc | t-c | 1 | 1 | All | 0 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.100 | 0.000046 |
ORF3a | 160 | Y160C | tAc | tGc | 1 | 1 | AY.102 | 0.000027 |
ORF3a | 160 | Y160C | tAc | tGc | 1 | 1 | AY.103 | 0.000006 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | AY.103 | 0.000006 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.105 | 0.000643 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.111 | 0.000183 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.116 | 0.000287 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.118 | 0.000063 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | AY.120 | 0.000037 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.16 | 0.00038 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | AY.25 | 0.000006 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | AY.25 | 0.000006 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | AY.29 | 0.000016 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.29 | 0.000016 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | AY.29 | 0.000016 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.33 | 0.000067 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.34.1 | 0.00051 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.39.1 | 0.00004 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | AY.4.2.1 | 0.000149 |
ORF3a | 160 | Y160N | Tac | Aac | 1 | 1 | AY.4.5 | 0.000107 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | AY.4.5 | 0.000107 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.4.5 | 0.000107 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | AY.44 | 0.000006 |
ORF3a | 160 | Y160X | taC | taA | 1 | 1 | AY.45 | 0.000122 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.45 | 0.000122 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.5.3 | 0.000337 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.52 | 0.000814 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.53 | 0.000288 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.59 | 0.00053 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | AY.6 | 0.000041 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.6 | 0.000041 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | AY.68 | 0.000274 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | AY.7 | 0.000196 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | AY.90 | 0.000684 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B | 0.000128 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B | 0.000128 |
ORF3a | 160 | Y160X | taC | taA | 1 | 1 | B.1 | 0.000009 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.1.157 | 0.000913 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.1.214 | 0.000055 |
ORF3a | 160 | Y160S | tAc | tCc | 1 | 1 | B.1.1.253 | 0.002506 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | B.1.1.306 | 0.000438 |
ORF3a | 160 | Y160C | tAc | tGc | 1 | 1 | B.1.1.317 | 0.000412 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.1.409 | 0.002833 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.1.525 | 0.005464 |
ORF3a | 160 | Y160X | taC | taA | 1 | 1 | B.1.1.7 | 0.000001 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.140 | 0.018868 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.160 | 0.000031 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.160.23 | 0.004831 |
ORF3a | 160 | Y160C | tAc | tGc | 1 | 1 | B.1.177 | 0.000013 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.177 | 0.000013 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.177.4 | 0.000211 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.177.51 | 0.004566 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.177.62 | 0.001192 |
ORF3a | 160 | Y160F | tAc | tTc | 1 | 1 | B.1.177.73 | 0.000566 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.177.73 | 0.000566 |
ORF3a | 160 | Y160del1 | tAc | t-c | 1 | 1 | B.1.2 | 0.000009 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.221 | 0.000071 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.258 | 0.000067 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.351 | 0.00003 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.351.5 | 0.0006 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.416.1 | 0.001563 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | B.1.429 | 0.000024 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.525 | 0.000113 |
ORF3a | 160 | Y160X | taC | taA | 1 | 1 | B.1.596 | 0.000087 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.596 | 0.000087 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.596 | 0.000087 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.617.1 | 0.000129 |
ORF3a | 160 | Y160F | tAc | tTc | 1 | 1 | B.1.617.2 | 0.000004 |
ORF3a | 160 | Y160H | Tac | Cac | 1 | 1 | B.1.617.2 | 0.000004 |
ORF3a | 160 | Y160Y | taC | taT | 1 | 1 | B.1.637 | 0.000073 |
ORF3a | 160 | Y160del | TAC | --- | 1 | 1 | B.1.638 | 0.052632 |
ORF3a | 160 | Y160N | Tac | Aac | 1 | 1 | B.6 | 0.00091 |
ORF3a | 160 | Y160C | tAc | tGc | 1 | 1 | C.35 | 0.000774 |
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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