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 | 899 | Y899Y | Y1717Y | syn | taC | taT | 604 | 604 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899H | Y1717H | nonsyn | Tac | Cac | 52 | 50 | 0.961538 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899H | Y1717H | nonsyn | TaC | CaT | 52 | 2 | 0.0384615 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899del | Y1717del | del | TAC | --- | 51 | 51 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899F | Y1717F | nonsyn | tAc | tTc | 5 | 5 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899X | Y1717X | nonsyn | taC | taA | 5 | 3 | 0.6 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899X | Y1717X | nonsyn | taC | taG | 5 | 2 | 0.4 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899C | Y1717C | nonsyn | tAc | tGc | 4 | 4 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899D | Y1717D | nonsyn | Tac | Gac | 2 | 2 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899Q | Y1717Q | nonsyn | TaC | CaA | 1 | 1 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899del2 | Y1717del2 | del | TAc | --c | 1 | 1 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899N | Y1717N | nonsyn | Tac | Aac | 1 | 1 | 1 | 5414-5416 |
ORF1ab/nsp3 | 899 | Y899del1 | Y1717del1 | del | Tac | -ac | 1 | 1 | 1 | 5414-5416 |
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 | 899 | Y899Y | taC | taT | 604 | 604 | All | 0.000116 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 78 | 78 | B.1.445 | 0.917647 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 77 | 77 | AY.43 | 0.000341 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 62 | 62 | AY.5 | 0.00128 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 56 | 56 | AY.4 | 0.000087 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 50 | 52 | All | 0.00001 |
ORF1ab/nsp3 | 899 | Y899H | TaC | CaT | 2 | 52 | All | 0 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 51 | 51 | All | 0.00001 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 40 | 40 | AY.46 | 0.004163 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 36 | 36 | B.1.1.7 | 0.000032 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 27 | 27 | AY.4 | 0.000042 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 25 | 25 | AY.44 | 0.000152 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 22 | 22 | B.1.160 | 0.000686 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 21 | 21 | B.1.621 | 0.001859 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 17 | 17 | B.1.1.7 | 0.000015 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 16 | 16 | AY.33 | 0.001068 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 15 | 15 | B.1.1 | 0.000272 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 15 | 15 | B.1.2 | 0.000132 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 14 | 14 | B.1.617.2 | 0.000053 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 11 | 11 | B.1.1.519 | 0.000437 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 10 | 10 | AY.29 | 0.000158 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 9 | 9 | B.1 | 0.000082 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 8 | 8 | AY.25 | 0.000048 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 6 | 6 | B.1.427 | 0.000303 |
ORF1ab/nsp3 | 899 | Y899F | tAc | tTc | 5 | 5 | All | 0.000001 |
ORF1ab/nsp3 | 899 | Y899X | taC | taA | 3 | 5 | All | 0.000001 |
ORF1ab/nsp3 | 899 | Y899X | taC | taG | 2 | 5 | All | 0 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 5 | 5 | AY.102 | 0.000133 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 5 | 5 | AY.118 | 0.000313 |
ORF1ab/nsp3 | 899 | Y899C | tAc | tGc | 4 | 4 | All | 0.000001 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 4 | 4 | AY.103 | 0.000025 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 4 | 4 | AY.20 | 0.000155 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 4 | 4 | AY.3 | 0.00004 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 4 | 4 | AY.47 | 0.000124 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 4 | 4 | B.1.637 | 0.000292 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 4 | 4 | P.1 | 0.000063 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 3 | 3 | AY.25 | 0.000018 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 3 | 3 | AY.46.6 | 0.000217 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 3 | 3 | B.1.1.434 | 0.001046 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 3 | 3 | B.1.2 | 0.000026 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 3 | 3 | B.1.617.2 | 0.000011 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 3 | 3 | P.1 | 0.000047 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 3 | 3 | P.1.14 | 0.000143 |
ORF1ab/nsp3 | 899 | Y899D | Tac | Gac | 2 | 2 | All | 0 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | AY.121 | 0.000271 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | AY.26 | 0.000057 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 2 | 2 | AY.43 | 0.000009 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | AY.6 | 0.000082 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | B | 0.000256 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 2 | 2 | B.1 | 0.000018 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | B.1.1.222 | 0.000408 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 2 | 2 | B.1.160 | 0.000062 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | B.1.177 | 0.000026 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | B.1.177.7 | 0.00033 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | B.1.243 | 0.000139 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 2 | 2 | B.1.36 | 0.000292 |
ORF1ab/nsp3 | 899 | Y899H | TaC | CaT | 2 | 2 | B.1.411 | 0.007407 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 2 | 2 | B.1.617.1 | 0.000258 |
ORF1ab/nsp3 | 899 | Y899C | tAc | tGc | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | A.2.2 | 0.001689 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 1 | 1 | A.2.4 | 0.003367 |
ORF1ab/nsp3 | 899 | Y899del2 | TAc | --c | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 899 | Y899Q | TaC | CaA | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 899 | Y899del1 | Tac | -ac | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 899 | Y899N | Tac | Aac | 1 | 1 | All | 0 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | AY.108 | 0.001103 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 1 | 1 | AY.116.1 | 0.000311 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 899 | Y899C | tAc | tGc | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.27 | 0.000065 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.3.1 | 0.000085 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.4.2 | 0.000022 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.45 | 0.000122 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | AY.66 | 0.00107 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.86 | 0.00083 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.9.1 | 0.000084 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.9.2 | 0.000037 |
ORF1ab/nsp3 | 899 | Y899del1 | Tac | -ac | 1 | 1 | AY.93 | 0.000273 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | AY.99.2 | 0.000092 |
ORF1ab/nsp3 | 899 | Y899X | taC | taA | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 899 | Y899D | Tac | Gac | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp3 | 899 | Y899X | taC | taG | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 899 | Y899D | Tac | Gac | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.1.129 | 0.009174 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.1.142 | 0.017544 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.1.163 | 0.007634 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.1.214 | 0.000055 |
ORF1ab/nsp3 | 899 | Y899F | tAc | tTc | 1 | 1 | B.1.1.300 | 0.010753 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.1.316 | 0.000925 |
ORF1ab/nsp3 | 899 | Y899X | taC | taA | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.157 | 0.002985 |
ORF1ab/nsp3 | 899 | Y899X | taC | taA | 1 | 1 | B.1.177 | 0.000013 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.177.16 | 0.000664 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.177.4 | 0.000211 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.177.54 | 0.000606 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.177.83 | 0.001481 |
ORF1ab/nsp3 | 899 | Y899F | tAc | tTc | 1 | 1 | B.1.184 | 0.058824 |
ORF1ab/nsp3 | 899 | Y899del2 | TAc | --c | 1 | 1 | B.1.23 | 0.006061 |
ORF1ab/nsp3 | 899 | Y899Q | TaC | CaA | 1 | 1 | B.1.258 | 0.000067 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.258.3 | 0.001675 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.319 | 0.003049 |
ORF1ab/nsp3 | 899 | Y899X | taC | taG | 1 | 1 | B.1.338 | 0.008621 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.36.8 | 0.001 |
ORF1ab/nsp3 | 899 | Y899F | tAc | tTc | 1 | 1 | B.1.36.8 | 0.001 |
ORF1ab/nsp3 | 899 | Y899N | Tac | Aac | 1 | 1 | B.1.362 | 0.001541 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.400 | 0.000429 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.438.1 | 0.000107 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.452 | 0.013699 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.499 | 0.00105 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.564 | 0.000426 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.577 | 0.000687 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.587 | 0.001898 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp3 | 899 | Y899F | tAc | tTc | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.1.620 | 0.000946 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | B.15 | 0.017544 |
ORF1ab/nsp3 | 899 | Y899Y | taC | taT | 1 | 1 | B.40 | 0.000364 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | C.36 | 0.000911 |
ORF1ab/nsp3 | 899 | Y899F | tAc | tTc | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 899 | Y899C | tAc | tGc | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | P.1.1 | 0.000318 |
ORF1ab/nsp3 | 899 | Y899del | TAC | --- | 1 | 1 | Q.2 | 0.000613 |
ORF1ab/nsp3 | 899 | Y899H | Tac | Cac | 1 | 1 | R.1 | 0.00009 |
![]() |
![]() |
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
|