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 | 695 | Y695Y | syn | taC | taT | 1002 | 1002 | 1 | 23645-23647 | |
S | 695 | Y695del | del | TAC | --- | 36 | 36 | 1 | 23645-23647 | |
S | 695 | Y695H | nonsyn | Tac | Cac | 11 | 11 | 1 | 23645-23647 | |
S | 695 | Y695C | nonsyn | tAc | tGc | 10 | 9 | 0.9 | 23645-23647 | |
S | 695 | Y695C | nonsyn | tAC | tGT | 10 | 1 | 0.1 | 23645-23647 | |
S | 695 | Y695X | nonsyn | taC | taA | 9 | 7 | 0.777778 | 23645-23647 | |
S | 695 | Y695X | nonsyn | taC | taG | 9 | 2 | 0.222222 | 23645-23647 | |
S | 695 | Y695S | nonsyn | tAc | tCc | 7 | 4 | 0.571429 | 23645-23647 | |
S | 695 | Y695S | nonsyn | TAc | AGc | 7 | 2 | 0.285714 | 23645-23647 | |
S | 695 | Y695S | nonsyn | tAC | tCA | 7 | 1 | 0.142857 | 23645-23647 | |
S | 695 | Y695F | nonsyn | tAc | tTc | 6 | 6 | 1 | 23645-23647 | |
S | 695 | Y695L | nonsyn | TAc | CTc | 6 | 2 | 0.333333 | 23645-23647 | |
S | 695 | Y695L | nonsyn | tAC | tTG | 6 | 2 | 0.333333 | 23645-23647 | |
S | 695 | Y695L | nonsyn | tAC | tTA | 6 | 1 | 0.166667 | 23645-23647 | |
S | 695 | Y695L | nonsyn | TAC | CTA | 6 | 1 | 0.166667 | 23645-23647 | |
S | 695 | Y695del1 | del | taC | ta- | 3 | 3 | 1 | 23645-23647 | |
S | 695 | Y695N | nonsyn | Tac | Aac | 2 | 2 | 1 | 23645-23647 | |
S | 695 | Y695D | nonsyn | Tac | Gac | 2 | 2 | 1 | 23645-23647 | |
S | 695 | Y695Q | nonsyn | TaC | CaA | 2 | 2 | 1 | 23645-23647 | |
S | 695 | Y695K | nonsyn | TaC | AaG | 2 | 1 | 0.5 | 23645-23647 | |
S | 695 | Y695P | nonsyn | TAc | CCc | 2 | 1 | 0.5 | 23645-23647 | |
S | 695 | Y695P | nonsyn | TAC | CCA | 2 | 1 | 0.5 | 23645-23647 | |
S | 695 | Y695T | nonsyn | TAc | ACc | 2 | 1 | 0.5 | 23645-23647 | |
S | 695 | Y695T | nonsyn | TAC | ACA | 2 | 1 | 0.5 | 23645-23647 | |
S | 695 | Y695K | nonsyn | TaC | AaA | 2 | 1 | 0.5 | 23645-23647 | |
S | 695 | Y695del2 | del | TAc | --c | 1 | 1 | 1 | 23645-23647 | |
S | 695 | Y695R | nonsyn | TAC | CGT | 1 | 1 | 1 | 23645-23647 |
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 |
S | 695 | Y695Y | taC | taT | 1002 | 1002 | All | 0.000192 |
S | 695 | Y695Y | taC | taT | 421 | 421 | B.1.160 | 0.01313 |
S | 695 | Y695Y | taC | taT | 143 | 143 | AY.3 | 0.001422 |
S | 695 | Y695Y | taC | taT | 134 | 134 | B.1.160.18 | 0.978102 |
S | 695 | Y695Y | taC | taT | 57 | 57 | AY.103 | 0.000354 |
S | 695 | Y695Y | taC | taT | 47 | 47 | B.1.1.7 | 0.000042 |
S | 695 | Y695del | TAC | --- | 36 | 36 | All | 0.000007 |
S | 695 | Y695Y | taC | taT | 34 | 34 | AY.29 | 0.000536 |
S | 695 | Y695Y | taC | taT | 30 | 30 | B.1.617.2 | 0.000113 |
S | 695 | Y695Y | taC | taT | 17 | 17 | AY.43 | 0.000075 |
S | 695 | Y695Y | taC | taT | 14 | 14 | AY.44 | 0.000085 |
S | 695 | Y695H | Tac | Cac | 11 | 11 | All | 0.000002 |
S | 695 | Y695C | tAc | tGc | 9 | 10 | All | 0.000002 |
S | 695 | Y695C | tAC | tGT | 1 | 10 | All | 0 |
S | 695 | Y695X | taC | taA | 7 | 9 | All | 0.000001 |
S | 695 | Y695X | taC | taG | 2 | 9 | All | 0 |
S | 695 | Y695Y | taC | taT | 9 | 9 | AY.42 | 0.000362 |
S | 695 | Y695Y | taC | taT | 8 | 8 | B.1 | 0.000073 |
S | 695 | Y695S | tAc | tCc | 4 | 7 | All | 0.000001 |
S | 695 | Y695S | TAc | AGc | 2 | 7 | All | 0 |
S | 695 | Y695S | tAC | tCA | 1 | 7 | All | 0 |
S | 695 | Y695Y | taC | taT | 7 | 7 | B.1.2 | 0.000062 |
S | 695 | Y695Y | taC | taT | 7 | 7 | B.1.221 | 0.000497 |
S | 695 | Y695F | tAc | tTc | 6 | 6 | All | 0.000001 |
S | 695 | Y695L | tAC | tTG | 2 | 6 | All | 0 |
S | 695 | Y695L | TAc | CTc | 2 | 6 | All | 0 |
S | 695 | Y695L | TAC | CTA | 1 | 6 | All | 0 |
S | 695 | Y695L | tAC | tTA | 1 | 6 | All | 0 |
S | 695 | Y695Y | taC | taT | 6 | 6 | AY.4 | 0.000009 |
S | 695 | Y695del | TAC | --- | 6 | 6 | B.1 | 0.000055 |
S | 695 | Y695X | taC | taA | 3 | 5 | 0.166667 | |
S | 695 | Y695S | TAc | AGc | 2 | 5 | 0.111111 | |
S | 695 | Y695L | tAC | tTG | 2 | 5 | 0.111111 | |
S | 695 | Y695X | taC | taG | 2 | 5 | 0.111111 | |
S | 695 | Y695S | tAc | tCc | 2 | 5 | 0.111111 | |
S | 695 | Y695L | TAC | CTA | 1 | 5 | 0.055556 | |
S | 695 | Y695L | TAc | CTc | 1 | 5 | 0.055556 | |
S | 695 | Y695S | tAC | tCA | 1 | 5 | 0.055556 | |
S | 695 | Y695L | tAC | tTA | 1 | 5 | 0.055556 | |
S | 695 | Y695Y | taC | taT | 5 | 5 | AY.102 | 0.000133 |
S | 695 | Y695Y | taC | taT | 5 | 5 | B.1.1.216 | 0.004452 |
S | 695 | Y695Y | taC | taT | 5 | 5 | B.1.160.32 | 0.021459 |
S | 695 | Y695C | tAc | tGc | 3 | 4 | AY.43 | 0.000013 |
S | 695 | Y695C | tAC | tGT | 1 | 4 | AY.43 | 0.000004 |
S | 695 | Y695F | tAc | tTc | 3 | 3 | 0.166667 | |
S | 695 | Y695del1 | taC | ta- | 3 | 3 | All | 0.000001 |
S | 695 | Y695del | TAC | --- | 3 | 3 | AY.25 | 0.000018 |
S | 695 | Y695Y | taC | taT | 3 | 3 | B.1.1 | 0.000054 |
S | 695 | Y695Y | taC | taT | 3 | 3 | B.1.1.39 | 0.001529 |
S | 695 | Y695Y | taC | taT | 3 | 3 | B.1.177 | 0.00004 |
S | 695 | Y695del | TAC | --- | 3 | 3 | P.1 | 0.000047 |
S | 695 | Y695del | TAC | --- | 3 | 3 | P.1.15 | 0.000697 |
S | 695 | Y695H | Tac | Cac | 2 | 2 | 0.111111 | |
S | 695 | Y695Q | TaC | CaA | 2 | 2 | 0.111111 | |
S | 695 | Y695P | TAC | CCA | 1 | 2 | 0.055556 | |
S | 695 | Y695P | TAc | CCc | 1 | 2 | 0.055556 | |
S | 695 | Y695T | TAC | ACA | 1 | 2 | 0.055556 | |
S | 695 | Y695T | TAc | ACc | 1 | 2 | 0.055556 | |
S | 695 | Y695N | Tac | Aac | 2 | 2 | All | 0 |
S | 695 | Y695Q | TaC | CaA | 2 | 2 | All | 0 |
S | 695 | Y695D | Tac | Gac | 2 | 2 | All | 0 |
S | 695 | Y695T | TAC | ACA | 1 | 2 | All | 0 |
S | 695 | Y695K | TaC | AaG | 1 | 2 | All | 0 |
S | 695 | Y695P | TAc | CCc | 1 | 2 | All | 0 |
S | 695 | Y695P | TAC | CCA | 1 | 2 | All | 0 |
S | 695 | Y695T | TAc | ACc | 1 | 2 | All | 0 |
S | 695 | Y695K | TaC | AaA | 1 | 2 | All | 0 |
S | 695 | Y695Y | taC | taT | 2 | 2 | AY.120 | 0.000074 |
S | 695 | Y695Y | taC | taT | 2 | 2 | AY.23 | 0.000139 |
S | 695 | Y695H | Tac | Cac | 2 | 2 | AY.4 | 0.000003 |
S | 695 | Y695del | TAC | --- | 2 | 2 | AY.43 | 0.000009 |
S | 695 | Y695del | TAC | --- | 2 | 2 | AY.44 | 0.000012 |
S | 695 | Y695Y | taC | taT | 2 | 2 | AY.47 | 0.000062 |
S | 695 | Y695X | taC | taA | 2 | 2 | B.1 | 0.000018 |
S | 695 | Y695del | TAC | --- | 2 | 2 | B.1.1.7 | 0.000002 |
S | 695 | Y695Y | taC | taT | 2 | 2 | B.1.429 | 0.000047 |
S | 695 | Y695del | TAC | --- | 2 | 2 | B.1.617.2 | 0.000008 |
S | 695 | Y695H | Tac | Cac | 2 | 2 | B.1.617.2 | 0.000008 |
S | 695 | Y695del | TAC | --- | 2 | 2 | B.1.621 | 0.000177 |
S | 695 | Y695K | TaC | AaA | 1 | 1 | 0.055556 | |
S | 695 | Y695N | Tac | Aac | 1 | 1 | 0.055556 | |
S | 695 | Y695del2 | TAc | --c | 1 | 1 | All | 0 |
S | 695 | Y695R | TAC | CGT | 1 | 1 | All | 0 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.100 | 0.000046 |
S | 695 | Y695del1 | taC | ta- | 1 | 1 | AY.102 | 0.000027 |
S | 695 | Y695del | TAC | --- | 1 | 1 | AY.103 | 0.000006 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.108 | 0.001103 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.116 | 0.000287 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.117 | 0.000085 |
S | 695 | Y695D | Tac | Gac | 1 | 1 | AY.117 | 0.000085 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.119 | 0.000035 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.19 | 0.00114 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.20 | 0.000039 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.25 | 0.000006 |
S | 695 | Y695S | tAc | tCc | 1 | 1 | AY.25 | 0.000006 |
S | 695 | Y695C | tAc | tGc | 1 | 1 | AY.3 | 0.00001 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.3.1 | 0.000085 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.30 | 0.000396 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.33 | 0.000067 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.39 | 0.000025 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.39.1.1 | 0.000725 |
S | 695 | Y695D | Tac | Gac | 1 | 1 | AY.4 | 0.000002 |
S | 695 | Y695N | Tac | Aac | 1 | 1 | AY.4 | 0.000002 |
S | 695 | Y695C | tAc | tGc | 1 | 1 | AY.4.2 | 0.000022 |
S | 695 | Y695R | TAC | CGT | 1 | 1 | AY.43 | 0.000004 |
S | 695 | Y695H | Tac | Cac | 1 | 1 | AY.43 | 0.000004 |
S | 695 | Y695F | tAc | tTc | 1 | 1 | AY.43 | 0.000004 |
S | 695 | Y695C | tAc | tGc | 1 | 1 | AY.44 | 0.000006 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.45 | 0.000122 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.5.3 | 0.000337 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.5.4 | 0.000277 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.53 | 0.000288 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.55 | 0.000917 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.61 | 0.000105 |
S | 695 | Y695del1 | taC | ta- | 1 | 1 | AY.61 | 0.000105 |
S | 695 | Y695Y | taC | taT | 1 | 1 | AY.74 | 0.000116 |
S | 695 | Y695del | TAC | --- | 1 | 1 | AY.84 | 0.000437 |
S | 695 | Y695K | TaC | AaG | 1 | 1 | AY.9.2 | 0.000037 |
S | 695 | Y695del | TAC | --- | 1 | 1 | AY.99 | 0.001049 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B | 0.000128 |
S | 695 | Y695H | Tac | Cac | 1 | 1 | B | 0.000128 |
S | 695 | Y695H | Tac | Cac | 1 | 1 | B.1 | 0.000009 |
S | 695 | Y695S | tAc | tCc | 1 | 1 | B.1.1 | 0.000018 |
S | 695 | Y695C | tAc | tGc | 1 | 1 | B.1.1 | 0.000018 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.1.318 | 0.000302 |
S | 695 | Y695del | TAC | --- | 1 | 1 | B.1.1.372 | 0.000689 |
S | 695 | Y695F | tAc | tTc | 1 | 1 | B.1.1.41 | 0.006329 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.1.432 | 0.001266 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.1.523 | 0.001563 |
S | 695 | Y695C | tAc | tGc | 1 | 1 | B.1.1.7 | 0.000001 |
S | 695 | Y695X | taC | taA | 1 | 1 | B.1.1.7 | 0.000001 |
S | 695 | Y695H | Tac | Cac | 1 | 1 | B.1.1.7 | 0.000001 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.177.23 | 0.003236 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.177.4 | 0.000211 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.177.60 | 0.000218 |
S | 695 | Y695del1 | taC | ta- | 1 | 1 | B.1.2 | 0.000009 |
S | 695 | Y695del | TAC | --- | 1 | 1 | B.1.2 | 0.000009 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.206 | 0.000816 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.221.3 | 0.000833 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.258 | 0.000067 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.258.17 | 0.000104 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.311 | 0.000275 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.351 | 0.00003 |
S | 695 | Y695H | Tac | Cac | 1 | 1 | B.1.351 | 0.00003 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.36 | 0.000146 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.468 | 0.005714 |
S | 695 | Y695del2 | TAc | --c | 1 | 1 | B.1.596 | 0.000087 |
S | 695 | Y695del | TAC | --- | 1 | 1 | B.1.596 | 0.000087 |
S | 695 | Y695Y | taC | taT | 1 | 1 | B.1.617.1 | 0.000129 |
S | 695 | Y695F | tAc | tTc | 1 | 1 | B.1.617.2 | 0.000004 |
S | 695 | Y695C | tAc | tGc | 1 | 1 | B.1.617.2 | 0.000004 |
S | 695 | Y695L | TAc | CTc | 1 | 1 | B.1.617.2 | 0.000004 |
S | 695 | Y695del | TAC | --- | 1 | 1 | B.1.620 | 0.000946 |
S | 695 | Y695del | TAC | --- | 1 | 1 | B.1.627 | 0.00202 |
S | 695 | Y695del | TAC | --- | 1 | 1 | B.1.638 | 0.052632 |
S | 695 | Y695X | taC | taA | 1 | 1 | B.6 | 0.00091 |
S | 695 | Y695del | TAC | --- | 1 | 1 | C.37 | 0.000116 |
S | 695 | Y695del | TAC | --- | 1 | 1 | P.1.13 | 0.000898 |
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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