CoV-GLUE | Mutations | Mutation
CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = H1539Y
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 | 1539 | H1539Y | H2357Y | nonsyn | Cat | Tat | 1669 | 1669 | 1 | 7334-7336 |
Details of the mutation H1539Y 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 | 1539 | H1539Y | Cat | Tat | 1669 | 1669 | All | 0.000319 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 661 | 661 | AP.1 | 0.992492 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 172 | 172 | AY.4 | 0.000268 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 101 | 101 | AY.103 | 0.000627 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 89 | 89 | B.1.1.7 | 0.00008 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 88 | 88 | B.1.258.17 | 0.00915 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 60 | 60 | B.1.617.2 | 0.000226 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 44 | 44 | B.1.2 | 0.000387 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 43 | 43 | AY.43 | 0.000191 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 23 | 23 | B.1 | 0.000211 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 19 | 19 | B.1.36.24 | 0.117284 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 16 | 16 | AY.44 | 0.000097 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 16 | 16 | B.1.160 | 0.000499 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 13 | 13 | AY.119 | 0.000459 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 13 | 13 | AY.35 | 0.00303 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 13 | 13 | B.1.429 | 0.000306 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 12 | 12 | AY.25 | 0.000072 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 11 | 11 | B.1.1 | 0.0002 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 10 | 10 | AY.33 | 0.000668 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 10 | 10 | AY.98 | 0.00079 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 10 | 10 | B.6.4 | 0.454545 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 8 | 8 | AY.113 | 0.001139 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 8 | 8 | B.1.177 | 0.000105 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 8 | 8 | B.1.596 | 0.000697 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 8 | 8 | P.1 | 0.000126 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 7 | 7 | AY.46.6 | 0.000505 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 7 | 7 | AY.5 | 0.000145 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 7 | 7 | B.35 | 0.054688 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 6 | 6 | B.1.1.519 | 0.000238 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 6 | 6 | B.1.551 | 0.007742 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 6 | 6 | R.1 | 0.00054 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 6 | 6 | W.3 | 0.031579 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 5 | 5 | AY.11 | 0.006693 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 5 | 5 | AY.120 | 0.000186 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 5 | 5 | AY.20 | 0.000194 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 5 | 5 | B.1.1.1 | 0.001633 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 5 | 5 | B.1.1.189 | 0.007564 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 5 | 5 | B.1.36 | 0.00073 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 5 | 5 | B.1.36.17 | 0.00247 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 4 | 4 | AY.102 | 0.000106 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 4 | 4 | AY.26 | 0.000113 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 4 | 4 | AY.46.4 | 0.000658 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 4 | 4 | AY.70 | 0.000834 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | 0.166667 | |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | AY.100 | 0.000138 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | AY.109 | 0.002219 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | AY.3 | 0.00003 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | AY.39 | 0.000074 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | AY.6 | 0.000123 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | B.1.438.1 | 0.000322 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | B.1.478 | 0.035294 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | B.1.575.1 | 0.007317 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 3 | 3 | B.1.621.1 | 0.001517 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | AY.116 | 0.000574 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | AY.38 | 0.000999 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | AY.42 | 0.00008 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | AY.71 | 0.00095 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | AY.74 | 0.000231 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | AY.98.1 | 0.000097 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | B.1.1.28 | 0.000622 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | B.1.177.41 | 0.005 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | B.1.221 | 0.000142 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | B.1.36.10 | 0.009569 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | B.1.36.8 | 0.002 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | B.1.576 | 0.001813 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | B.6.6 | 0.001778 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 2 | 2 | C.36.3 | 0.001134 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | A.3 | 0.002096 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.107 | 0.000466 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.108 | 0.001103 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.117 | 0.000085 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.14 | 0.000088 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.16 | 0.00038 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.16.1 | 0.00047 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.23 | 0.00007 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.29 | 0.000016 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.30 | 0.000396 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.34 | 0.000097 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.34.1 | 0.00051 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.4.5 | 0.000107 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.46.1 | 0.001027 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.46.5 | 0.000198 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.52 | 0.000814 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.56 | 0.001605 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.67 | 0.000464 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.75 | 0.000056 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.75.1 | 0.00018 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.82 | 0.001357 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.83 | 0.001724 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.84 | 0.000437 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.9.2.1 | 0.001976 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | AY.99.2 | 0.000092 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.1.10 | 0.001115 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.1.219 | 0.005 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.1.220 | 0.001859 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.1.317 | 0.000412 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.1.33 | 0.000421 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.113 | 0.015625 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.177.23 | 0.003236 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.177.60 | 0.000218 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.177.65 | 0.000665 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.177.8 | 0.000752 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.192 | 0.009259 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.234 | 0.000132 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.240 | 0.000216 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.258 | 0.000067 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.349 | 0.000715 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.351 | 0.00003 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.351.2 | 0.000303 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.396 | 0.000706 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.409 | 0.000781 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.427 | 0.00005 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.499 | 0.00105 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.564 | 0.000426 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.565 | 0.00081 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.577 | 0.000687 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.582 | 0.000491 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.617.3 | 0.002985 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.621 | 0.000089 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.9.5 | 0.005682 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | B.1.93 | 0.000934 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | C.37 | 0.000116 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | D.2 | 0.000075 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | P.1.15 | 0.000232 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | P.2 | 0.000187 |
| ORF1ab/nsp3 | 1539 | H1539Y | Cat | Tat | 1 | 1 | P.3 | 0.001595 |
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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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