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/nsp4 | 300 | Y300Y | Y3063Y | syn | taT | taC | 3726 | 3726 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300S | Y3063S | nonsyn | tAt | tCt | 277 | 277 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300C | Y3063C | nonsyn | tAt | tGt | 96 | 96 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300H | Y3063H | nonsyn | Tat | Cat | 67 | 66 | 0.985075 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300H | Y3063H | nonsyn | TaT | CaC | 67 | 1 | 0.0149254 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300del | Y3063del | del | TAT | --- | 59 | 59 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300N | Y3063N | nonsyn | Tat | Aat | 46 | 46 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300del1 | Y3063del1 | del | taT | ta- | 6 | 6 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300F | Y3063F | nonsyn | tAt | tTt | 6 | 6 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300X | Y3063X | nonsyn | taT | taA | 5 | 4 | 0.8 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300X | Y3063X | nonsyn | taT | taG | 5 | 1 | 0.2 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300K | Y3063K | nonsyn | TaT | AaA | 2 | 2 | 1 | 9452-9454 |
ORF1ab/nsp4 | 300 | Y300D | Y3063D | nonsyn | Tat | Gat | 1 | 1 | 1 | 9452-9454 |
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/nsp4 | 300 | Y300Y | taT | taC | 3726 | 3726 | All | 0.000713 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1700 | 1700 | B.1.1.7 | 0.001522 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1685 | 1685 | AY.4 | 0.002623 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 277 | 277 | All | 0.000053 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 256 | 256 | L.3 | 0.907801 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 96 | 96 | All | 0.000018 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 93 | 93 | B.1.617.2 | 0.00035 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 66 | 67 | All | 0.000013 |
ORF1ab/nsp4 | 300 | Y300H | TaT | CaC | 1 | 67 | All | 0 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 59 | 59 | All | 0.000011 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 58 | 58 | P.1.1 | 0.018424 |
ORF1ab/nsp4 | 300 | Y300N | Tat | Aat | 46 | 46 | All | 0.000009 |
ORF1ab/nsp4 | 300 | Y300N | Tat | Aat | 45 | 45 | B.1.1.7 | 0.00004 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 37 | 37 | AY.102 | 0.000981 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 31 | 31 | B.1.1.7 | 0.000028 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 29 | 29 | B.1.111 | 0.034078 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 25 | 25 | AY.103 | 0.000155 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 19 | 19 | B.1.1.7 | 0.000017 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 18 | 18 | B.1.1 | 0.000327 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 16 | 16 | AY.42 | 0.000644 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 16 | 16 | AY.86 | 0.013278 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 14 | 14 | AY.44 | 0.000085 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 13 | 13 | AY.5 | 0.000268 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 13 | 13 | B.1.525 | 0.001471 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 11 | 11 | B.1 | 0.000101 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 9 | 9 | B.1.177.5 | 0.01118 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 7 | 7 | AY.43 | 0.000031 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 7 | 7 | B.1.177 | 0.000092 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 7 | 7 | P.1 | 0.00011 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 7 | 7 | R.1 | 0.00063 |
ORF1ab/nsp4 | 300 | Y300del1 | taT | ta- | 6 | 6 | All | 0.000001 |
ORF1ab/nsp4 | 300 | Y300F | tAt | tTt | 6 | 6 | All | 0.000001 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 6 | 6 | AY.44 | 0.000037 |
ORF1ab/nsp4 | 300 | Y300X | taT | taA | 4 | 5 | All | 0.000001 |
ORF1ab/nsp4 | 300 | Y300X | taT | taG | 1 | 5 | All | 0 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 5 | 5 | AY.34.1 | 0.00255 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 5 | 5 | B.1 | 0.000046 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 4 | 5 | B.1.617.2 | 0.000015 |
ORF1ab/nsp4 | 300 | Y300H | TaT | CaC | 1 | 5 | B.1.617.2 | 0.000004 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 4 | 4 | AY.26 | 0.000113 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 4 | 4 | AY.39 | 0.000099 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 4 | 4 | AY.46.4 | 0.000658 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 4 | 4 | B.1.1.7 | 0.000004 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 3 | 3 | AY.103 | 0.000019 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 3 | 3 | AY.4 | 0.000005 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 3 | 3 | AY.4.5 | 0.000322 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 3 | 3 | B.1.1 | 0.000054 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 3 | 3 | B.1.1.10 | 0.003344 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 3 | 3 | B.1.36 | 0.000438 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 3 | 3 | B.1.526 | 0.000071 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 3 | 3 | C.36.3 | 0.001702 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 3 | 3 | C.37 | 0.000348 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 3 | 3 | P.1 | 0.000047 |
ORF1ab/nsp4 | 300 | Y300K | TaT | AaA | 2 | 2 | All | 0 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 2 | 2 | AY.111 | 0.000366 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 2 | 2 | AY.119 | 0.000071 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 2 | 2 | AY.25 | 0.000012 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 2 | 2 | AY.3 | 0.00002 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 2 | 2 | AY.4 | 0.000003 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 2 | 2 | AY.44 | 0.000012 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 2 | 2 | AY.45 | 0.000243 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 2 | 2 | AY.46 | 0.000208 |
ORF1ab/nsp4 | 300 | Y300del1 | taT | ta- | 2 | 2 | AY.46.2 | 0.001271 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 2 | 2 | B.1.1.214 | 0.000111 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 2 | 2 | B.1.1.519 | 0.000079 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 2 | 2 | B.1.429 | 0.000047 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 2 | 2 | B.1.526 | 0.000047 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 2 | 2 | B.1.617.2 | 0.000008 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 2 | 2 | R.1 | 0.00018 |
ORF1ab/nsp4 | 300 | Y300D | Tat | Gat | 1 | 1 | 0.055556 | |
ORF1ab/nsp4 | 300 | Y300D | Tat | Gat | 1 | 1 | All | 0 |
ORF1ab/nsp4 | 300 | Y300X | taT | taA | 1 | 1 | AY.102 | 0.000027 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.116.1 | 0.000311 |
ORF1ab/nsp4 | 300 | Y300K | TaT | AaA | 1 | 1 | AY.117 | 0.000085 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 1 | 1 | AY.119 | 0.000035 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 1 | 1 | AY.120 | 0.000037 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | AY.13 | 0.000161 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.20 | 0.000039 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.23 | 0.00007 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 1 | 1 | AY.25 | 0.000006 |
ORF1ab/nsp4 | 300 | Y300X | taT | taA | 1 | 1 | AY.26 | 0.000028 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | AY.3 | 0.00001 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | AY.36 | 0.000148 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.38 | 0.000499 |
ORF1ab/nsp4 | 300 | Y300del1 | taT | ta- | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp4 | 300 | Y300F | tAt | tTt | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp4 | 300 | Y300X | taT | taA | 1 | 1 | AY.4 | 0.000002 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | AY.4.5 | 0.000107 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | AY.43 | 0.000004 |
ORF1ab/nsp4 | 300 | Y300F | tAt | tTt | 1 | 1 | AY.44 | 0.000006 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 1 | 1 | AY.48 | 0.000465 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | AY.61 | 0.000105 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.75 | 0.000056 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | AY.88 | 0.000884 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | AY.9 | 0.000068 |
ORF1ab/nsp4 | 300 | Y300del1 | taT | ta- | 1 | 1 | B.1.1 | 0.000018 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.1.153 | 0.001095 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | B.1.1.221 | 0.010101 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.1.266 | 0.012195 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | B.1.1.311 | 0.000358 |
ORF1ab/nsp4 | 300 | Y300del1 | taT | ta- | 1 | 1 | B.1.1.312 | 0.001912 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | B.1.1.37 | 0.000193 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | B.1.1.372 | 0.000689 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 1 | 1 | B.1.1.409 | 0.002833 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.1.519 | 0.00004 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.1.63 | 0.000386 |
ORF1ab/nsp4 | 300 | Y300F | tAt | tTt | 1 | 1 | B.1.1.7 | 0.000001 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 1 | 1 | B.1.1.70 | 0.000341 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.160 | 0.000031 |
ORF1ab/nsp4 | 300 | Y300del1 | taT | ta- | 1 | 1 | B.1.160.23 | 0.004831 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | B.1.177.19 | 0.001431 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.177.60 | 0.000218 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | B.1.177.75 | 0.001041 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.2 | 0.000009 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 1 | 1 | B.1.349 | 0.000715 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.351 | 0.00003 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.36.29 | 0.000517 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.369 | 0.000285 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | B.1.427 | 0.00005 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.428 | 0.00102 |
ORF1ab/nsp4 | 300 | Y300C | tAt | tGt | 1 | 1 | B.1.438.1 | 0.000107 |
ORF1ab/nsp4 | 300 | Y300K | TaT | AaA | 1 | 1 | B.1.466.2 | 0.000391 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | B.1.561 | 0.000397 |
ORF1ab/nsp4 | 300 | Y300X | taT | taA | 1 | 1 | B.1.564 | 0.000426 |
ORF1ab/nsp4 | 300 | Y300H | Tat | Cat | 1 | 1 | B.1.564 | 0.000426 |
ORF1ab/nsp4 | 300 | Y300N | Tat | Aat | 1 | 1 | B.1.596 | 0.000087 |
ORF1ab/nsp4 | 300 | Y300F | tAt | tTt | 1 | 1 | B.1.612 | 0.002653 |
ORF1ab/nsp4 | 300 | Y300F | tAt | tTt | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | B.1.617.2 | 0.000004 |
ORF1ab/nsp4 | 300 | Y300S | tAt | tCt | 1 | 1 | B.1.636 | 0.006711 |
ORF1ab/nsp4 | 300 | Y300X | taT | taG | 1 | 1 | B.1.637 | 0.000073 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | B.15 | 0.017544 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | B.34 | 0.013699 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | B.4.4 | 0.018868 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | C.35 | 0.000774 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | D.2 | 0.000075 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp4 | 300 | Y300F | tAt | tTt | 1 | 1 | P.1 | 0.000016 |
ORF1ab/nsp4 | 300 | Y300del | TAT | --- | 1 | 1 | Q.1 | 0.000126 |
ORF1ab/nsp4 | 300 | Y300Y | taT | taC | 1 | 1 | Q.1 | 0.000126 |
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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