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/nsp12 | 525 | D525D | D4917D | syn | gaT | gaC | 663 | 663 | 1 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525N | D4917N | nonsyn | Gat | Aat | 229 | 226 | 0.9869 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525N | D4917N | nonsyn | GaT | AaC | 229 | 3 | 0.0131004 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525del | D4917del | del | GAT | --- | 43 | 43 | 1 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525Y | D4917Y | nonsyn | Gat | Tat | 14 | 14 | 1 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525E | D4917E | nonsyn | gaT | gaA | 12 | 8 | 0.666667 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525E | D4917E | nonsyn | gaT | gaG | 12 | 4 | 0.333333 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525V | D4917V | nonsyn | gAt | gTt | 8 | 6 | 0.75 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525V | D4917V | nonsyn | gAT | gTA | 8 | 2 | 0.25 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525A | D4917A | nonsyn | gAt | gCt | 6 | 4 | 0.666667 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525A | D4917A | nonsyn | gAT | gCA | 6 | 2 | 0.333333 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525H | D4917H | nonsyn | Gat | Cat | 5 | 3 | 0.6 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525H | D4917H | nonsyn | GaT | CaC | 5 | 2 | 0.4 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525G | D4917G | nonsyn | gAt | gGt | 4 | 4 | 1 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525del1 | D4917del1 | del | Gat | -at | 1 | 1 | 1 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525C | D4917C | nonsyn | GAt | TGt | 1 | 1 | 1 | 15013-15015 |
ORF1ab/nsp12 | 525 | D525I | D4917I | nonsyn | GAT | ATC | 1 | 1 | 1 | 15013-15015 |
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/nsp12 | 525 | D525D | gaT | gaC | 663 | 663 | All | 0.000127 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 337 | 337 | B.1.1.7 | 0.000302 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 226 | 229 | All | 0.000043 |
ORF1ab/nsp12 | 525 | D525N | GaT | AaC | 3 | 229 | All | 0.000001 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 167 | 167 | AY.4 | 0.00026 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 95 | 95 | B.1.177 | 0.001251 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 57 | 57 | C.4 | 0.57 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 43 | 43 | All | 0.000008 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 24 | 24 | B.1.1.435 | 0.827586 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 22 | 22 | AY.25 | 0.000132 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 15 | 15 | AY.117 | 0.001268 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 14 | 14 | All | 0.000003 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 13 | 13 | AY.9.2 | 0.000477 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaA | 8 | 12 | All | 0.000002 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaG | 4 | 12 | All | 0.000001 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 12 | 12 | B.1.1.280 | 0.037037 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 11 | 11 | B.1.239 | 0.013431 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 10 | 10 | B.1.1.7 | 0.000009 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 10 | 10 | B.1.617.2 | 0.000038 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 9 | 9 | AY.44 | 0.000055 |
ORF1ab/nsp12 | 525 | D525V | gAt | gTt | 6 | 8 | All | 0.000001 |
ORF1ab/nsp12 | 525 | D525V | gAT | gTA | 2 | 8 | All | 0 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 8 | 8 | AY.25 | 0.000048 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 7 | 7 | AY.103 | 0.000043 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 7 | 7 | AY.4 | 0.000011 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 7 | 7 | B.1 | 0.000064 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 7 | 7 | B.1.568 | 0.007778 |
ORF1ab/nsp12 | 525 | D525A | gAt | gCt | 4 | 6 | All | 0.000001 |
ORF1ab/nsp12 | 525 | D525A | gAT | gCA | 2 | 6 | All | 0 |
ORF1ab/nsp12 | 525 | D525V | gAt | gTt | 3 | 5 | 0.166667 | |
ORF1ab/nsp12 | 525 | D525V | gAT | gTA | 2 | 5 | 0.111111 | |
ORF1ab/nsp12 | 525 | D525H | Gat | Cat | 3 | 5 | All | 0.000001 |
ORF1ab/nsp12 | 525 | D525H | GaT | CaC | 2 | 5 | All | 0 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 5 | 5 | AY.39 | 0.000124 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 5 | 5 | AY.43 | 0.000022 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaA | 4 | 5 | AY.44 | 0.000024 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaG | 1 | 5 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 4 | 5 | B.1.617.2 | 0.000015 |
ORF1ab/nsp12 | 525 | D525N | GaT | AaC | 1 | 5 | B.1.617.2 | 0.000004 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 4 | 4 | 0.222222 | |
ORF1ab/nsp12 | 525 | D525A | gAT | gCA | 2 | 4 | 0.111111 | |
ORF1ab/nsp12 | 525 | D525A | gAt | gCt | 2 | 4 | 0.111111 | |
ORF1ab/nsp12 | 525 | D525G | gAt | gGt | 4 | 4 | All | 0.000001 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 3 | 4 | AY.44 | 0.000018 |
ORF1ab/nsp12 | 525 | D525N | GaT | AaC | 1 | 4 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 4 | 4 | B.1.1 | 0.000073 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 4 | 4 | B.1.1.1 | 0.001307 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 3 | 3 | AY.103 | 0.000019 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 3 | 3 | AY.107 | 0.001398 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 3 | 3 | AY.29 | 0.000047 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 3 | 3 | B.1 | 0.000027 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 3 | 3 | B.1.427 | 0.000151 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 3 | 3 | B.1.637 | 0.000219 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaA | 2 | 2 | 0.111111 | |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | 0.111111 | |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 2 | 2 | AY.100 | 0.000092 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 2 | 2 | AY.39 | 0.000049 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 2 | 2 | AY.43 | 0.000009 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | AZ.6 | 0.016807 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | B.1.1.170 | 0.002494 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | B.1.221 | 0.000142 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | B.1.351 | 0.000059 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | B.1.36.1 | 0.002281 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | C.37 | 0.000232 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 2 | 2 | P.1 | 0.000032 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | A | 0.000387 |
ORF1ab/nsp12 | 525 | D525V | gAt | gTt | 1 | 1 | A.2.4 | 0.003367 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | AD.2 | 0.000219 |
ORF1ab/nsp12 | 525 | D525del1 | Gat | -at | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 525 | D525C | GAt | TGt | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 525 | D525I | GAT | ATC | 1 | 1 | All | 0 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | AY.100 | 0.000046 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | AY.110 | 0.000113 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp12 | 525 | D525H | Gat | Cat | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | AY.29 | 0.000016 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp12 | 525 | D525G | gAt | gGt | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp12 | 525 | D525G | gAt | gGt | 1 | 1 | AY.39 | 0.000025 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | AY.39.1 | 0.00004 |
ORF1ab/nsp12 | 525 | D525G | gAt | gGt | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | AY.4.4 | 0.000409 |
ORF1ab/nsp12 | 525 | D525A | gAt | gCt | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | AY.42 | 0.00004 |
ORF1ab/nsp12 | 525 | D525H | GaT | CaC | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 525 | D525V | gAt | gTt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | AY.5 | 0.000021 |
ORF1ab/nsp12 | 525 | D525A | gAt | gCt | 1 | 1 | AY.51 | 0.000909 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaA | 1 | 1 | AY.54 | 0.000095 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | AY.65 | 0.000533 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | AY.67 | 0.000464 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp12 | 525 | D525C | GAt | TGt | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | AY.75.1 | 0.00018 |
ORF1ab/nsp12 | 525 | D525H | GaT | CaC | 1 | 1 | AY.84 | 0.000437 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | AY.85 | 0.000427 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | AY.99 | 0.001049 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | B.1 | 0.000009 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp12 | 525 | D525H | Gat | Cat | 1 | 1 | B.1.1.198 | 0.001468 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp12 | 525 | D525del1 | Gat | -at | 1 | 1 | B.1.1.306 | 0.000438 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaG | 1 | 1 | B.1.1.369 | 0.000446 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.160.23 | 0.004831 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.160.7 | 0.002079 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | B.1.160.9 | 0.007194 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | B.1.177.48 | 0.003125 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaG | 1 | 1 | B.1.177.48 | 0.003125 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.177.68 | 0.015152 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.177.76 | 0.002494 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | B.1.177.87 | 0.000728 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | B.1.236 | 0.002053 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | B.1.367 | 0.000792 |
ORF1ab/nsp12 | 525 | D525V | gAt | gTt | 1 | 1 | B.1.416 | 0.001269 |
ORF1ab/nsp12 | 525 | D525D | gaT | gaC | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | B.1.429 | 0.000024 |
ORF1ab/nsp12 | 525 | D525N | Gat | Aat | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaG | 1 | 1 | B.1.525 | 0.000113 |
ORF1ab/nsp12 | 525 | D525H | Gat | Cat | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp12 | 525 | D525N | GaT | AaC | 1 | 1 | B.1.568 | 0.001111 |
ORF1ab/nsp12 | 525 | D525G | gAt | gGt | 1 | 1 | B.1.595 | 0.000261 |
ORF1ab/nsp12 | 525 | D525I | GAT | ATC | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp12 | 525 | D525E | gaT | gaA | 1 | 1 | B.6.6 | 0.000889 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp12 | 525 | D525Y | Gat | Tat | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | P.1.4 | 0.000977 |
ORF1ab/nsp12 | 525 | D525del | GAT | --- | 1 | 1 | Q.8 | 0.000165 |
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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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