CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp16 : CodonNum = 1

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
ORF1ab/nsp161S1AS6799AnonsynTctGct8888120659-20661
ORF1ab/nsp161S1TS6799TnonsynTctAct63620.98412720659-20661
ORF1ab/nsp161S1TS6799TnonsynTcTAcC6310.01587320659-20661
ORF1ab/nsp161S1delS6799deldelTCT---5555120659-20661
ORF1ab/nsp161S1del1S6799del1delTct-ct49460.93877620659-20661
ORF1ab/nsp161S1del1S6799del1delTcT-cC4910.020408220659-20661
ORF1ab/nsp161S1del1S6799del1deltcTtc-4910.020408220659-20661
ORF1ab/nsp161S1del1S6799del1deltCtt-t4910.020408220659-20661
ORF1ab/nsp161S1FS6799FnonsyntCttTt28260.92857120659-20661
ORF1ab/nsp161S1FS6799FnonsyntCTtTC2820.071428620659-20661
ORF1ab/nsp161S1YS6799YnonsyntCttAt88120659-20661
ORF1ab/nsp161S1PS6799PnonsynTctCct66120659-20661
ORF1ab/nsp161S1LS6799LnonsyntCTtTA11120659-20661
ORF1ab/nsp161S1CS6799CnonsyntCttGt11120659-20661
ORF1ab/nsp161S1DS6799DnonsynTCTGAC11120659-20661

Details of the mutation no 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/nsp161S1ATctGct8888All0.000017
ORF1ab/nsp161S1TTctAct6263All0.000012
ORF1ab/nsp161S1TTcTAcC163All0
ORF1ab/nsp161S1StcTtcC6262B.1.177.361
ORF1ab/nsp161S1StcTtcC6262B.1.177.390.953846
ORF1ab/nsp161S1delTCT---5555All0.000011
ORF1ab/nsp161S1del1Tct-ct4649All0.000009
ORF1ab/nsp161S1del1tcTtc-149All0
ORF1ab/nsp161S1del1tCtt-t149All0
ORF1ab/nsp161S1del1TcT-cC149All0
ORF1ab/nsp161S1StcTtcC4646B.1.160.300.136905
ORF1ab/nsp161S1StcTtcC4242B.1.2210.002983
ORF1ab/nsp161S1del1Tct-ct3637B.1.1.70.000032
ORF1ab/nsp161S1del1tCtt-t137B.1.1.70.000001
ORF1ab/nsp161S1StcTtcC3233B.1.1600.000998
ORF1ab/nsp161S1StcTtcA133B.1.1600.000031
ORF1ab/nsp161S1StcTtcC3333B.1.177.370.891892
ORF1ab/nsp161S1FtCttTt2628All0.000005
ORF1ab/nsp161S1FtCTtTC228All0
ORF1ab/nsp161S1ATctGct2525AY.40.000039
ORF1ab/nsp161S1TTctAct2525AY.40.000039
ORF1ab/nsp161S1ATctGct2424B.1.1.70.000021
ORF1ab/nsp161S1TTctAct1919AY.4.50.002042
ORF1ab/nsp161S1delTCT---1919B.1.1.70.000017
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/nsp161S1delTCT---880.444444
ORF1ab/nsp161S1YtCttAt88All0.000002
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/nsp161S1ATctGct77B.1.617.20.000026
ORF1ab/nsp161S1PTctCct66All0.000001
ORF1ab/nsp161S1StcTtcC66B0.000767
ORF1ab/nsp161S1StcTtcC66B.1.160.320.025751
ORF1ab/nsp161S1TTctAct55AY.90.000338
ORF1ab/nsp161S1StcTtcC55B.1.416.10.007812
ORF1ab/nsp161S1ATctGct44AY.440.000024
ORF1ab/nsp161S1TTctAct44AY.80.002424
ORF1ab/nsp161S1FtCttTt44B.1.1.70.000004
ORF1ab/nsp161S1StcTtcC44B.1.177.730.002265
ORF1ab/nsp161S1ATctGct33A0.001161
ORF1ab/nsp161S1ATctGct33AY.430.000013
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/nsp161S1ATctGct33B.1.177.70.000495
ORF1ab/nsp161S1del1Tct-ct33B.1.177.820.001432
ORF1ab/nsp161S1StcTtcC33B.1.177.860.00055
ORF1ab/nsp161S1StcTtcC33B.1.2600.010033
ORF1ab/nsp161S1delTCT---33B.1.617.20.000011
ORF1ab/nsp161S1StcTtcC12AY.1030.000006
ORF1ab/nsp161S1StcTtcA12AY.1030.000006
ORF1ab/nsp161S1TTctAct22AY.1200.000074
ORF1ab/nsp161S1ATctGct22AY.39.10.000079
ORF1ab/nsp161S1delTCT---22AY.4.50.000215
ORF1ab/nsp161S1TTctAct22AY.580.001815
ORF1ab/nsp161S1StcTtcC22AY.840.000875
ORF1ab/nsp161S1YtCttAt22B.10.000018
ORF1ab/nsp161S1ATctGct22B.10.000018
ORF1ab/nsp161S1FtCttTt22B.10.000018
ORF1ab/nsp161S1FtCTtTC12B.1.10.000018
ORF1ab/nsp161S1FtCttTt12B.1.10.000018
ORF1ab/nsp161S1YtCttAt22B.1.1.70.000002
ORF1ab/nsp161S1del1Tct-ct22B.1.1600.000062
ORF1ab/nsp161S1StcTtcC22B.1.160.100.016129
ORF1ab/nsp161S1FtCTtTC12B.1.1770.000013
ORF1ab/nsp161S1FtCttTt12B.1.1770.000013
ORF1ab/nsp161S1StcTtcC22B.1.177.520.003515
ORF1ab/nsp161S1StcTtcC22B.1.177.570.000562
ORF1ab/nsp161S1StcTtcC22B.1.20.000018
ORF1ab/nsp161S1StcTtcC22B.1.2220.003384
ORF1ab/nsp161S1FtCttTt22B.1.2340.000264
ORF1ab/nsp161S1StcTtcC22B.1.2400.000431
ORF1ab/nsp161S1del1Tct-ct22B.1.3510.000059
ORF1ab/nsp161S1StcTtcC22B.1.6090.000959
ORF1ab/nsp161S1StcTtcC22B.1.617.20.000008
ORF1ab/nsp161S1FtCttTt22D.20.00015
ORF1ab/nsp161S1ATctGct22P.10.000032
ORF1ab/nsp161S1FtCttTt11A.20.000662
ORF1ab/nsp161S1LtCTtTA11All0
ORF1ab/nsp161S1CtCttGt11All0
ORF1ab/nsp161S1DTCTGAC11All0
ORF1ab/nsp161S1ATctGct11AY.1030.000006
ORF1ab/nsp161S1del1tcTtc-11AY.1130.000142
ORF1ab/nsp161S1PTctCct11AY.1170.000085
ORF1ab/nsp161S1StcTtcG11AY.1200.000037
ORF1ab/nsp161S1FtCttTt11AY.16.10.00047
ORF1ab/nsp161S1TTctAct11AY.170.008197
ORF1ab/nsp161S1delTCT---11AY.250.000006
ORF1ab/nsp161S1FtCttTt11AY.250.000006
ORF1ab/nsp161S1ATctGct11AY.250.000006
ORF1ab/nsp161S1del1Tct-ct11AY.250.000006
ORF1ab/nsp161S1ATctGct11AY.270.000065
ORF1ab/nsp161S1ATctGct11AY.34.10.00051
ORF1ab/nsp161S1YtCttAt11AY.390.000025
ORF1ab/nsp161S1FtCttTt11AY.40.000002
ORF1ab/nsp161S1delTCT---11AY.40.000002
ORF1ab/nsp161S1YtCttAt11AY.40.000002
ORF1ab/nsp161S1StcTtcA11AY.4.50.000107
ORF1ab/nsp161S1DTCTGAC11AY.430.000004
ORF1ab/nsp161S1delTCT---11AY.440.000006
ORF1ab/nsp161S1FtCttTt11AY.440.000006
ORF1ab/nsp161S1ATctGct11AY.450.000122
ORF1ab/nsp161S1StcTtcG11AY.450.000122
ORF1ab/nsp161S1ATctGct11AY.470.000031
ORF1ab/nsp161S1ATctGct11AY.50.000021
ORF1ab/nsp161S1del1Tct-ct11AY.520.000814
ORF1ab/nsp161S1delTCT---11AY.670.000464
ORF1ab/nsp161S1delTCT---11AY.840.000437
ORF1ab/nsp161S1TTctAct11AY.870.000833
ORF1ab/nsp161S1StcTtcA11AY.9.20.000037
ORF1ab/nsp161S1StcTtcC11AY.940.000443
ORF1ab/nsp161S1FtCttTt11AY.980.000079
ORF1ab/nsp161S1StcTtcC11AY.98.10.000048
ORF1ab/nsp161S1delTCT---11AY.990.001049
ORF1ab/nsp161S1ATctGct11AY.99.10.001553
ORF1ab/nsp161S1YtCttAt11B0.000128
ORF1ab/nsp161S1TTcTAcC11B.10.000009
ORF1ab/nsp161S1delTCT---11B.1.10.000018
ORF1ab/nsp161S1StcTtcC11B.1.1.10.000327
ORF1ab/nsp161S1StcTtcC11B.1.1.1410.002012
ORF1ab/nsp161S1StcTtcC11B.1.1.1700.001247
ORF1ab/nsp161S1delTCT---11B.1.1.1700.001247
ORF1ab/nsp161S1StcTtcC11B.1.1.1890.001513
ORF1ab/nsp161S1ATctGct11B.1.1.330.000421
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/nsp161S1FtCttTt11B.1.1.590.006494
ORF1ab/nsp161S1TTctAct11B.1.1.70.000001
ORF1ab/nsp161S1delTCT---11B.1.1.700.000341
ORF1ab/nsp161S1StcTtcC11B.1.1040.00369
ORF1ab/nsp161S1ATctGct11B.1.1390.000733
ORF1ab/nsp161S1StcTtcC11B.1.160.160.000929
ORF1ab/nsp161S1StcTtcC11B.1.160.260.002421
ORF1ab/nsp161S1StcTtcG11B.1.160.290.004219
ORF1ab/nsp161S1delTCT---11B.1.177.170.000821
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/nsp161S1del1TcT-cC11B.1.177.60.000977
ORF1ab/nsp161S1StcTtcC11B.1.177.650.000665
ORF1ab/nsp161S1delTCT---11B.1.177.730.000566
ORF1ab/nsp161S1StcTtcC11B.1.177.770.000726
ORF1ab/nsp161S1FtCttTt11B.1.177.800.001912
ORF1ab/nsp161S1delTCT---11B.1.177.830.001481
ORF1ab/nsp161S1StcTtcC11B.1.177.870.000728
ORF1ab/nsp161S1delTCT---11B.1.177.870.000728
ORF1ab/nsp161S1StcTtcC11B.1.177.890.02439
ORF1ab/nsp161S1CtCttGt11B.1.20.000009
ORF1ab/nsp161S1FtCttTt11B.1.20.000009
ORF1ab/nsp161S1delTCT---11B.1.20.000009
ORF1ab/nsp161S1ATctGct11B.1.20.000009
ORF1ab/nsp161S1FtCttTt11B.1.2060.000816
ORF1ab/nsp161S1StcTtcC11B.1.214.30.007143
ORF1ab/nsp161S1StcTtcC11B.1.2330.014085
ORF1ab/nsp161S1StcTtcC11B.1.2370.004975
ORF1ab/nsp161S1ATctGct11B.1.2430.00007
ORF1ab/nsp161S1delTCT---11B.1.2580.000067
ORF1ab/nsp161S1StcTtcC11B.1.2840.013158
ORF1ab/nsp161S1FtCttTt11B.1.3360.002439
ORF1ab/nsp161S1PTctCct11B.1.3510.00003
ORF1ab/nsp161S1ATctGct11B.1.36.250.002208
ORF1ab/nsp161S1StcTtcC11B.1.36.90.003215
ORF1ab/nsp161S1LtCTtTA11B.1.4160.001269
ORF1ab/nsp161S1FtCttTt11B.1.4290.000024
ORF1ab/nsp161S1StcTtcC11B.1.4730.019231
ORF1ab/nsp161S1StcTtcC11B.1.5250.000113
ORF1ab/nsp161S1delTCT---11B.1.5250.000113
ORF1ab/nsp161S1PTctCct11B.1.5260.000024
ORF1ab/nsp161S1delTCT---11B.1.5260.000024
ORF1ab/nsp161S1StcTtcG11B.1.5260.000024
ORF1ab/nsp161S1StcTtcC11B.1.5330.009615
ORF1ab/nsp161S1StcTtcC11B.1.5610.000397
ORF1ab/nsp161S1delTCT---11B.1.5610.000397
ORF1ab/nsp161S1delTCT---11B.1.5960.000087
ORF1ab/nsp161S1TTctAct11B.1.5990.00365
ORF1ab/nsp161S1StcTtcC11B.1.617.10.000129
ORF1ab/nsp161S1YtCttAt11B.1.617.20.000004
ORF1ab/nsp161S1TTctAct11B.1.617.20.000004
ORF1ab/nsp161S1PTctCct11B.1.617.20.000004
ORF1ab/nsp161S1delTCT---11B.1.6200.000946
ORF1ab/nsp161S1StcTtcC11B.1.780.008547
ORF1ab/nsp161S1FtCttTt11B.200.023256
ORF1ab/nsp161S1PTctCct11B.30.000831
ORF1ab/nsp161S1delTCT---11B.340.013699
ORF1ab/nsp161S1PTctCct11B.4.50.011905
ORF1ab/nsp161S1FtCttTt11B.60.00091
ORF1ab/nsp161S1StcTtcC11K.10.02381
ORF1ab/nsp161S1StcTtcC11P.10.000016
ORF1ab/nsp161S1delTCT---11P.1.150.000232
ORF1ab/nsp161S1delTCT---11P.1.70.000319
ORF1ab/nsp161S1StcTtcC11P.30.001595
ORF1ab/nsp161S1del1Tct-ct11R.10.00009
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

CoV-GLUE uses sequence data from GISAID. GISAID data provided via this web application is subject to GISAID's Terms and Conditions.