CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp16 : Mut = S1S

Details of the codons used for the mutation across all lineages (CodonProp is the proportion each codon is used for this AA mutation):

ORFCodonNumMutORF1abMutMutTypeRefCodonMutCodonAACountCodonCountCodonPropGenome Position
ORF1ab/nsp161S1SS6799SsyntcTtcC17353173330.99884720659-20661
ORF1ab/nsp161S1SS6799SsyntcTtcA17353140.00080677720659-20661
ORF1ab/nsp161S1SS6799SsyntcTtcG1735350.00028813520659-20661
ORF1ab/nsp161S1SS6799SsynTCtAGt1735310.000057626920659-20661

Details of the mutation S1S within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF1ab/nsp161S1StcTtcC1733317353All0.003315
ORF1ab/nsp161S1StcTtcA1417353All0.000003
ORF1ab/nsp161S1StcTtcG517353All0.000001
ORF1ab/nsp161S1STCtAGt117353All0
ORF1ab/nsp161S1StcTtcC65666566B.1.177.120.996056
ORF1ab/nsp161S1StcTtcC45734573B.1.1770.060215
ORF1ab/nsp161S1StcTtcC17381738B.1.177.440.90192
ORF1ab/nsp161S1StcTtcC13441344B.1.177.350.928818
ORF1ab/nsp161S1StcTtcC10741074B.1.177.420.960644
ORF1ab/nsp161S1StcTtcC643643B.1.177.430.949778
ORF1ab/nsp161S1StcTtcC398398B.1.177.410.995
ORF1ab/nsp161S1StcTtcC203203B.10.001859
ORF1ab/nsp161S1StcTtcC191191B.1.177.400.984536
ORF1ab/nsp161S1StcTtcC9595B.1.177.380.989583
ORF1ab/nsp161S1StcTtcC6262B.1.177.361
ORF1ab/nsp161S1StcTtcC6262B.1.177.390.953846
ORF1ab/nsp161S1StcTtcC4646B.1.160.300.136905
ORF1ab/nsp161S1StcTtcC4242B.1.2210.002983
ORF1ab/nsp161S1StcTtcC3233B.1.1600.000998
ORF1ab/nsp161S1StcTtcA133B.1.1600.000031
ORF1ab/nsp161S1StcTtcC3333B.1.177.370.891892
ORF1ab/nsp161S1StcTtcC1919B.1.360.002772
ORF1ab/nsp161S1StcTtcC1717B.1.10.000308
ORF1ab/nsp161S1StcTtcC1217B.1.2580.000799
ORF1ab/nsp161S1StcTtcA517B.1.2580.000333
ORF1ab/nsp161S1StcTtcC1515B.1.177.310.172414
ORF1ab/nsp161S1StcTtcC1414AY.140.001232
ORF1ab/nsp161S1StcTtcC711B.1.1.70.000006
ORF1ab/nsp161S1StcTtcA211B.1.1.70.000002
ORF1ab/nsp161S1STCtAGt111B.1.1.70.000001
ORF1ab/nsp161S1StcTtcG111B.1.1.70.000001
ORF1ab/nsp161S1StcTtcC1010B.1.177.60.009766
ORF1ab/nsp161S1StcTtcC88AY.200.000311
ORF1ab/nsp161S1StcTtcC78AY.40.000011
ORF1ab/nsp161S1StcTtcA18AY.40.000002
ORF1ab/nsp161S1StcTtcC88AY.880.007073
ORF1ab/nsp161S1StcTtcC88B.1.4290.000188
ORF1ab/nsp161S1StcTtcC77B.1.1.390.003568
ORF1ab/nsp161S1StcTtcC77B.1.177.90.009321
ORF1ab/nsp161S1StcTtcC66B0.000767
ORF1ab/nsp161S1StcTtcC66B.1.160.320.025751
ORF1ab/nsp161S1StcTtcC55B.1.416.10.007812
ORF1ab/nsp161S1StcTtcC44B.1.177.730.002265
ORF1ab/nsp161S1StcTtcA23AY.430.000009
ORF1ab/nsp161S1StcTtcC13AY.430.000004
ORF1ab/nsp161S1StcTtcC33AY.440.000018
ORF1ab/nsp161S1StcTtcC33B.1.1.700.001023
ORF1ab/nsp161S1StcTtcC33B.1.177.450.001144
ORF1ab/nsp161S1StcTtcC33B.1.177.860.00055
ORF1ab/nsp161S1StcTtcC33B.1.2600.010033
ORF1ab/nsp161S1StcTtcA12AY.1030.000006
ORF1ab/nsp161S1StcTtcC12AY.1030.000006
ORF1ab/nsp161S1StcTtcC22AY.840.000875
ORF1ab/nsp161S1StcTtcC22B.1.160.100.016129
ORF1ab/nsp161S1StcTtcC22B.1.177.520.003515
ORF1ab/nsp161S1StcTtcC22B.1.177.570.000562
ORF1ab/nsp161S1StcTtcC22B.1.20.000018
ORF1ab/nsp161S1StcTtcC22B.1.2220.003384
ORF1ab/nsp161S1StcTtcC22B.1.2400.000431
ORF1ab/nsp161S1StcTtcC22B.1.6090.000959
ORF1ab/nsp161S1StcTtcC22B.1.617.20.000008
ORF1ab/nsp161S1StcTtcG11AY.1200.000037
ORF1ab/nsp161S1StcTtcA11AY.4.50.000107
ORF1ab/nsp161S1StcTtcG11AY.450.000122
ORF1ab/nsp161S1StcTtcA11AY.9.20.000037
ORF1ab/nsp161S1StcTtcC11AY.940.000443
ORF1ab/nsp161S1StcTtcC11AY.98.10.000048
ORF1ab/nsp161S1StcTtcC11B.1.1.10.000327
ORF1ab/nsp161S1StcTtcC11B.1.1.1410.002012
ORF1ab/nsp161S1StcTtcC11B.1.1.1700.001247
ORF1ab/nsp161S1StcTtcC11B.1.1.1890.001513
ORF1ab/nsp161S1StcTtcC11B.1.1.3430.020833
ORF1ab/nsp161S1StcTtcC11B.1.1.370.000193
ORF1ab/nsp161S1StcTtcC11B.1.1.3720.000689
ORF1ab/nsp161S1StcTtcC11B.1.1.5210.005348
ORF1ab/nsp161S1StcTtcC11B.1.1040.00369
ORF1ab/nsp161S1StcTtcC11B.1.160.160.000929
ORF1ab/nsp161S1StcTtcC11B.1.160.260.002421
ORF1ab/nsp161S1StcTtcG11B.1.160.290.004219
ORF1ab/nsp161S1StcTtcC11B.1.177.170.000821
ORF1ab/nsp161S1StcTtcC11B.1.177.210.000076
ORF1ab/nsp161S1StcTtcC11B.1.177.230.003236
ORF1ab/nsp161S1StcTtcC11B.1.177.500.004695
ORF1ab/nsp161S1StcTtcC11B.1.177.650.000665
ORF1ab/nsp161S1StcTtcC11B.1.177.770.000726
ORF1ab/nsp161S1StcTtcC11B.1.177.870.000728
ORF1ab/nsp161S1StcTtcC11B.1.177.890.02439
ORF1ab/nsp161S1StcTtcC11B.1.214.30.007143
ORF1ab/nsp161S1StcTtcC11B.1.2330.014085
ORF1ab/nsp161S1StcTtcC11B.1.2370.004975
ORF1ab/nsp161S1StcTtcC11B.1.2840.013158
ORF1ab/nsp161S1StcTtcC11B.1.36.90.003215
ORF1ab/nsp161S1StcTtcC11B.1.4730.019231
ORF1ab/nsp161S1StcTtcC11B.1.5250.000113
ORF1ab/nsp161S1StcTtcG11B.1.5260.000024
ORF1ab/nsp161S1StcTtcC11B.1.5330.009615
ORF1ab/nsp161S1StcTtcC11B.1.5610.000397
ORF1ab/nsp161S1StcTtcC11B.1.617.10.000129
ORF1ab/nsp161S1StcTtcC11B.1.780.008547
ORF1ab/nsp161S1StcTtcC11K.10.02381
ORF1ab/nsp161S1StcTtcC11P.10.000016
ORF1ab/nsp161S1StcTtcC11P.30.001595
ORF1ab/nsp161S1StcTtcC11Z.10.00289

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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