CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 289

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
S289V289InonsynGtaAta3048430484122427-22429
S289V289LnonsynGtaTta136311420.83785822427-22429
S289V289LnonsynGtaCta13632210.16214222427-22429
S289V289VsyngtAgtG3993340.83709322427-22429
S289V289VsyngtAgtT399460.11528822427-22429
S289V289VsyngtAgtC399190.04761922427-22429
S289V289deldelGTA---162162122427-22429
S289V289AnonsyngTagCa27230.85185222427-22429
S289V289AnonsyngTAgCC2730.11111122427-22429
S289V289AnonsyngTAgCG2710.03703722427-22429
S289V289GnonsyngTagGa1080.822427-22429
S289V289GnonsyngTAgGC1010.122427-22429
S289V289GnonsyngTAgGG1010.122427-22429
S289V289del1delGta-ta720.28571422427-22429
S289V289del1delGtA-tN710.14285722427-22429
S289V289del1delGtA-tT710.14285722427-22429
S289V289del1delGTA-CG710.14285722427-22429
S289V289del1delgtAgt-710.14285722427-22429
S289V289del1delGTA-NN710.14285722427-22429
S289V289del2delgTAg--640.66666722427-22429
S289V289del2delGTa--a610.16666722427-22429
S289V289del2delGTA--N610.16666722427-22429
S289V289EnonsyngTagAa430.7522427-22429
S289V289TnonsynGTaACa430.7522427-22429
S289V289EnonsyngTAgAG410.2522427-22429
S289V289TnonsynGTAACG410.2522427-22429
S289V289PnonsynGTACCG320.66666722427-22429
S289V289PnonsynGTACCT310.33333322427-22429
S289V289MnonsynGtAAtG22122427-22429
S289V289DnonsyngTAgAC11122427-22429
S289V289XnonsynGTATAG11122427-22429
S289V289SnonsynGTaTCa11122427-22429

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
S289V289IGtaAta3048430484All0.00583
S289V289IGtaAta2885928859AY.470.897664
S289V289LGtaTta11421363All0.000218
S289V289LGtaCta2211363All0.000042
S289V289LGtaTta425538AY.40.000661
S289V289LGtaCta113538AY.40.000176
S289V289VgtAgtG334399All0.000064
S289V289VgtAgtT46399All0.000009
S289V289VgtAgtC19399All0.000004
S289V289IGtaAta352352AY.750.01972
S289V289IGtaAta303303B.1.617.20.001141
S289V289IGtaAta282282B.1.1.70.000252
S289V289delGTA---162162All0.000031
S289V289VgtAgtG155155AY.1200.005763
S289V289LGtaTta86103B.1.1.70.000077
S289V289LGtaCta17103B.1.1.70.000015
S289V289LGtaTta9595AY.600.089118
S289V289IGtaAta8787B.1.1.3480.069268
S289V289VgtAgtG7084B.1.1.70.000063
S289V289VgtAgtC1084B.1.1.70.000009
S289V289VgtAgtT484B.1.1.70.000004
S289V289LGtaTta7983AY.430.00035
S289V289LGtaCta483AY.430.000018
S289V289IGtaAta7777B.1.3690.021962
S289V289LGtaTta6868AY.690.012694
S289V289IGtaAta5656AY.75.10.010097
S289V289LGtaTta5053B.1.617.20.000188
S289V289LGtaCta353B.1.617.20.000011
S289V289IGtaAta4949AY.440.000298
S289V289LGtaTta4646AY.1030.000286
S289V289IGtaAta4040B.1.10.000726
S289V289delGTA---4040B.1.1.70.000036
S289V289LGtaTta3232AY.1110.005861
S289V289LGtaTta3131AY.4.20.000672
S289V289LGtaCta2828AY.710.013302
S289V289AgTagCa2327All0.000004
S289V289AgTAgCC327All0.000001
S289V289AgTAgCG127All0
S289V289LGtaTta2526AY.470.000778
S289V289LGtaCta126AY.470.000031
S289V289IGtaAta2626AY.620.011329
S289V289IGtaAta2424AY.610.002515
S289V289IGtaAta2323AY.430.000102
S289V289IGtaAta2222AY.1030.000137
S289V289IGtaAta2222AY.40.000034
S289V289delGTA---2222B.10.000202
S289V289VgtAgtG1919B.1.1770.00025
S289V289LGtaCta1618C.370.001857
S289V289LGtaTta218C.370.000232
S289V289IGtaAta1616AY.250.000096
S289V289LGtaTta916AY.30.00009
S289V289LGtaCta716AY.30.00007
S289V289IGtaAta1616B.10.000147
S289V289IGtaAta1515AY.410.004409
S289V289LGtaTta1214AY.250.000072
S289V289LGtaCta214AY.250.000012
S289V289VgtAgtG613AY.40.000009
S289V289VgtAgtT613AY.40.000009
S289V289VgtAgtC113AY.40.000002
S289V289VgtAgtG612B.10.000055
S289V289VgtAgtT612B.10.000055
S289V289IGtaAta1212B.1.20.000106
S289V289LGtaTta1111AY.440.000067
S289V289VgtAgtG711B.1.20.000062
S289V289VgtAgtT411B.1.20.000035
S289V289GgTagGa810All0.000002
S289V289GgTAgGG110All0
S289V289GgTAgGC110All0
S289V289LGtaTta710AY.1020.000186
S289V289LGtaCta310AY.1020.00008
S289V289IGtaAta99AY.1020.000239
S289V289LGtaTta79AY.200.000272
S289V289LGtaCta29AY.200.000078
S289V289LGtaTta79AY.390.000173
S289V289LGtaCta29AY.390.000049
S289V289LGtaTta99AY.9.20.000331
S289V289IGtaAta99B.1.1770.000119
S289V289IGtaAta99B.1.2430.000626
S289V289VgtAgtT78AY.460.000729
S289V289VgtAgtG18AY.460.000104
S289V289IGtaAta88AY.930.002185
S289V289LGtaTta88B.10.000073
S289V289delGTA---88B.1.3510.000238
S289V289del1Gta-ta27All0
S289V289del1gtAgt-17All0
S289V289del1GtA-tT17All0
S289V289del1GTA-CG17All0
S289V289del1GTA-NN17All0
S289V289del1GtA-tN17All0
S289V289IGtaAta77AY.1170.000592
S289V289LGtaTta67AY.1200.000223
S289V289LGtaCta17AY.1200.000037
S289V289IGtaAta77AY.120.20.008997
S289V289LGtaCta47AY.4.50.00043
S289V289LGtaTta37AY.4.50.000322
S289V289LGtaTta77AY.50.000145
S289V289del2gTAg--46All0.000001
S289V289del2GTa--a16All0
S289V289del2GTA--N16All0
S289V289VgtAgtG46AY.250.000024
S289V289VgtAgtT26AY.250.000012
S289V289delGTA---66AY.290.000095
S289V289IGtaAta66AY.30.00006
S289V289VgtAgtG36AY.430.000013
S289V289VgtAgtC26AY.430.000009
S289V289VgtAgtT16AY.430.000004
S289V289IGtaAta66AY.450.00073
S289V289LGtaTta56AY.90.000338
S289V289LGtaCta16AY.90.000068
S289V289IGtaAta66B.1.1060.1875
S289V289LGtaCta46B.1.20.000035
S289V289LGtaTta26B.1.20.000018
S289V289delGTA---66B.1.5250.000679
S289V289IGtaAta55AY.260.000142
S289V289LGtaTta45AY.290.000063
S289V289LGtaCta15AY.290.000016
S289V289VgtAgtG55AY.370.00158
S289V289VgtAgtG55AY.390.000124
S289V289delGTA---55AY.430.000022
S289V289IGtaAta55AY.540.000477
S289V289LGtaTta55B.1.1770.000066
S289V289delGTA---55B.1.617.20.000019
S289V289delGTA---55P.10.000079
S289V289LGtaTta55P.10.000079
S289V289VgtAgtG440.222222
S289V289TGTaACa34All0.000001
S289V289EgTagAa34All0.000001
S289V289TGTAACG14All0
S289V289EgTAgAG14All0
S289V289LGtaTta44AY.1000.000184
S289V289LGtaTta44AY.260.000113
S289V289LGtaTta44AY.330.000267
S289V289IGtaAta44AY.390.000099
S289V289IGtaAta44AY.39.10.000158
S289V289IGtaAta44AY.710.0019
S289V289LGtaTta44AY.98.10.000194
S289V289VgtAgtG44B.1.1.370.000771
S289V289LGtaTta44B.1.177.170.003284
S289V289LGtaTta44B.1.2430.000278
S289V289delGTA---44B.1.351.20.00121
S289V289IGtaAta44B.1.416.10.00625
S289V289IGtaAta44B.1.5640.001704
S289V289VgtAgtG24B.1.617.20.000008
S289V289VgtAgtT24B.1.617.20.000008
S289V289PGTACCG23All0
S289V289PGTACCT13All0
S289V289VgtAgtT33AY.10.001187
S289V289IGtaAta33AY.1090.002219
S289V289IGtaAta33AY.1100.000338
S289V289IGtaAta33AY.1190.000106
S289V289VgtAgtG33AY.200.000117
S289V289LGtaTta33AY.230.000209
S289V289LGtaTta33AY.270.000194
S289V289delGTA---33AY.30.00003
S289V289VgtAgtG23AY.30.00002
S289V289VgtAgtC13AY.30.00001
S289V289IGtaAta33AY.330.0002
S289V289delGTA---33AY.40.000005
S289V289LGtaTta33AY.420.000121
S289V289AgTAgCC23AY.430.000009
S289V289EgTagAa23AY.430.000009
S289V289EgTAgAG13AY.430.000004
S289V289AgTagCa13AY.430.000004
S289V289LGtaTta33AY.460.000312
S289V289IGtaAta33AY.50.000062
S289V289IGtaAta33AY.9.20.00011
S289V289IGtaAta33B0.000383
S289V289AgTagCa33B.10.000027
S289V289VgtAgtG33B.1.10.000054
S289V289delGTA---33B.1.10.000054
S289V289IGtaAta33B.1.1.2690.00406
S289V289delGTA---33B.1.20.000026
S289V289AgTagCa33B.1.3510.000089
S289V289IGtaAta33B.1.3510.000089
S289V289IGtaAta33B.1.6210.000266
S289V289IGtaAta33P.1.140.000143
S289V289MGtAAtG220.111111
S289V289delGTA---220.111111
S289V289IGtaAta220.111111
S289V289GgTagGa220.111111
S289V289MGtAAtG22All0
S289V289IGtaAta22AY.1000.000092
S289V289VgtAgtC12AY.1000.000046
S289V289VgtAgtG12AY.1000.000046
S289V289VgtAgtG22AY.1030.000012
S289V289VgtAgtG22AY.1130.000285
S289V289IGtaAta22AY.1140.000462
S289V289LGtaCta12AY.1170.000085
S289V289LGtaTta12AY.1170.000085
S289V289LGtaTta22AY.1180.000125
S289V289IGtaAta22AY.1180.000125
S289V289LGtaTta22AY.1190.000071
S289V289IGtaAta22AY.1200.000074
S289V289LGtaTta22AY.1210.000271
S289V289AgTagCa22AY.1210.000271
S289V289IGtaAta22AY.190.002281
S289V289LGtaTta22AY.190.002281
S289V289IGtaAta22AY.240.000862
S289V289delGTA---22AY.250.000012
S289V289LGtaCta22AY.29.10.000441
S289V289LGtaTta22AY.3.10.000171
S289V289IGtaAta22AY.34.10.00102
S289V289LGtaTta22AY.4.10.001475
S289V289VgtAgtT22AY.420.00008
S289V289VgtAgtG22AY.440.000012
S289V289LGtaTta22AY.450.000243
S289V289IGtaAta22AY.46.20.001271
S289V289LGtaTta22AY.46.50.000397
S289V289delGTA---22AY.46.60.000144
S289V289VgtAgtT12AY.50.000021
S289V289VgtAgtG12AY.50.000021
S289V289IGtaAta22AY.60.000082
S289V289LGtaTta12AY.670.000464
S289V289LGtaCta12AY.670.000464
S289V289LGtaTta22AY.700.000417
S289V289AgTAgCC12AY.9.20.000037
S289V289GgTAgGC12AY.9.20.000037
S289V289GgTAgGG12AY.9.20.000037
S289V289AgTAgCG12AY.9.20.000037
S289V289IGtaAta22AY.950.001522
S289V289VgtAgtC12AY.98.10.000048
S289V289VgtAgtG12AY.98.10.000048
S289V289delGTA---22AY.990.002099
S289V289del2gTAg--22B.10.000018
S289V289LGtaCta22B.1.10.000036
S289V289GgTagGa22B.1.1.70.000002
S289V289AgTagCa22B.1.1.70.000002
S289V289del1gtAgt-12B.1.1.70.000001
S289V289del1Gta-ta12B.1.1.70.000001
S289V289LGtaTta12B.1.1600.000031
S289V289LGtaCta12B.1.1600.000031
S289V289delGTA---22B.1.1770.000026
S289V289IGtaAta22B.1.177.820.000955
S289V289LGtaTta22B.1.177.90.002663
S289V289IGtaAta22B.1.2580.000133
S289V289delGTA---22B.1.2600.006689
S289V289VgtAgtT12B.1.3510.00003
S289V289VgtAgtG12B.1.3510.00003
S289V289IGtaAta22B.1.4270.000101
S289V289delGTA---22B.1.4560.006536
S289V289LGtaTta22B.1.5260.000047
S289V289VgtAgtG12B.1.5260.000024
S289V289VgtAgtT12B.1.5260.000024
S289V289delGTA---22B.1.5760.001813
S289V289IGtaAta22B.1.6280.000705
S289V289VgtAgtC12B.400.000364
S289V289VgtAgtT12B.400.000364
S289V289AgTagCa22D.20.00015
S289V289delGTA---22P.1.150.000465
S289V289LGtaTta22P.1.170.000324
S289V289LGtaTta22Q.70.002222
S289V289delGTA---11A0.000387
S289V289VgtAgtG11A.10.000282
S289V289AgTagCa11A.2.40.003367
S289V289delGTA---11A.2.50.000499
S289V289SGTaTCa11All0
S289V289DgTAgAC11All0
S289V289XGTATAG11All0
S289V289LGtaTta11AY.10.000396
S289V289IGtaAta11AY.100.00053
S289V289delGTA---11AY.1010.00049
S289V289LGtaTta11AY.1040.001984
S289V289VgtAgtT11AY.1050.000643
S289V289IGtaAta11AY.1050.000643
S289V289IGtaAta11AY.1060.000335
S289V289LGtaTta11AY.1060.000335
S289V289IGtaAta11AY.1080.001103
S289V289delGTA---11AY.1080.001103
S289V289delGTA---11AY.1100.000113
S289V289delGTA---11AY.1130.000142
S289V289delGTA---11AY.1170.000085
S289V289delGTA---11AY.1180.000063
S289V289VgtAgtG11AY.120.20.001285
S289V289IGtaAta11AY.1210.000135
S289V289IGtaAta11AY.16.10.00047
S289V289IGtaAta11AY.180.010101
S289V289IGtaAta11AY.200.000039
S289V289IGtaAta11AY.23.10.000417
S289V289LGtaTta11AY.240.000431
S289V289VgtAgtG11AY.270.000065
S289V289IGtaAta11AY.290.000016
S289V289IGtaAta11AY.29.10.000221
S289V289VgtAgtT11AY.3.10.000085
S289V289delGTA---11AY.330.000067
S289V289LGtaTta11AY.340.000097
S289V289LGtaTta11AY.34.10.00051
S289V289IGtaAta11AY.350.000233
S289V289LGtaTta11AY.360.000148
S289V289del2GTa--a11AY.360.000148
S289V289IGtaAta11AY.380.000499
S289V289LGtaCta11AY.39.10.00004
S289V289AgTagCa11AY.40.000002
S289V289IGtaAta11AY.4.20.000022
S289V289AgTagCa11AY.4.20.000022
S289V289AgTagCa11AY.400.000964
S289V289PGTACCG11AY.420.00004
S289V289DgTAgAC11AY.430.000004
S289V289del1GTA-CG11AY.430.000004
S289V289delGTA---11AY.440.000006
S289V289TGTAACG11AY.440.000006
S289V289GgTagGa11AY.440.000006
S289V289XGTATAG11AY.440.000006
S289V289IGtaAta11AY.460.000104
S289V289VgtAgtG11AY.46.40.000165
S289V289delGTA---11AY.470.000031
S289V289IGtaAta11AY.5.40.000277
S289V289delGTA---11AY.510.000909
S289V289IGtaAta11AY.530.000288
S289V289LGtaTta11AY.540.000095
S289V289VgtAgtG11AY.550.000917
S289V289IGtaAta11AY.550.000917
S289V289IGtaAta11AY.560.001605
S289V289delGTA---11AY.590.00053
S289V289LGtaTta11AY.590.00053
S289V289IGtaAta11AY.590.00053
S289V289LGtaTta11AY.60.000041
S289V289delGTA---11AY.610.000105
S289V289LGtaTta11AY.610.000105
S289V289GgTagGa11AY.620.000436
S289V289IGtaAta11AY.650.000533
S289V289delGTA---11AY.670.000464
S289V289IGtaAta11AY.670.000464
S289V289IGtaAta11AY.680.000274
S289V289LGtaTta11AY.680.000274
S289V289IGtaAta11AY.740.000116
S289V289LGtaTta11AY.750.000056
S289V289del2gTAg--11AY.750.000056
S289V289LGtaTta11AY.770.001127
S289V289IGtaAta11AY.80.000606
S289V289delGTA---11AY.840.000437
S289V289IGtaAta11AY.840.000437
S289V289IGtaAta11AY.880.000884
S289V289IGtaAta11AY.90.000068
S289V289delGTA---11AY.90.000068
S289V289delGTA---11AY.9.20.000037
S289V289VgtAgtG11AY.9.20.000037
S289V289delGTA---11AY.900.000684
S289V289IGtaAta11AY.900.000684
S289V289LGtaTta11AY.920.000287
S289V289LGtaTta11AY.930.000273
S289V289del2gTAg--11AY.98.10.000048
S289V289IGtaAta11AY.990.001049
S289V289LGtaTta11AY.99.20.000092
S289V289AgTagCa11B0.000128
S289V289VgtAgtG11B0.000128
S289V289del1Gta-ta11B.10.000009
S289V289LGtaTta11B.1.1.1760.000439
S289V289VgtAgtT11B.1.1.2070.001182
S289V289LGtaTta11B.1.1.2840.000107
S289V289AgTagCa11B.1.1.2990.012195
S289V289delGTA---11B.1.1.3010.001179
S289V289LGtaTta11B.1.1.3110.000358
S289V289VgtAgtG11B.1.1.3220.008772
S289V289VgtAgtG11B.1.1.3480.000796
S289V289LGtaTta11B.1.1.370.000193
S289V289IGtaAta11B.1.1.4420.018519
S289V289LGtaCta11B.1.1.4860.001577
S289V289LGtaTta11B.1.1.490.017544
S289V289VgtAgtC11B.1.1.5190.00004
S289V289LGtaTta11B.1.1.5190.00004
S289V289IGtaAta11B.1.1.5230.001563
S289V289VgtAgtG11B.1.1.550.012987
S289V289LGtaTta11B.1.1.590.006494
S289V289SGTaTCa11B.1.1.70.000001
S289V289TGTaACa11B.1.1.70.000001
S289V289IGtaAta11B.1.1570.002985
S289V289VgtAgtC11B.1.1570.002985
S289V289IGtaAta11B.1.177.120.000152
S289V289LGtaTta11B.1.177.180.00116
S289V289delGTA---11B.1.177.60.000977
S289V289VgtAgtG11B.1.177.600.000218
S289V289LGtaTta11B.1.177.630.002703
S289V289delGTA---11B.1.177.830.001481
S289V289delGTA---11B.1.177.870.000728
S289V289AgTagCa11B.1.20.000009
S289V289IGtaAta11B.1.2400.000216
S289V289VgtAgtG11B.1.2580.000067
S289V289VgtAgtG11B.1.258.170.000104
S289V289VgtAgtG11B.1.2790.000514
S289V289del2GTA--N11B.1.3510.00003
S289V289PGTACCT11B.1.3510.00003
S289V289LGtaTta11B.1.3510.00003
S289V289LGtaCta11B.1.360.000146
S289V289delGTA---11B.1.360.000146
S289V289delGTA---11B.1.416.10.001563
S289V289AgTagCa11B.1.4230.010204
S289V289VgtAgtG11B.1.4270.00005
S289V289VgtAgtG11B.1.4290.000024
S289V289delGTA---11B.1.4290.000024
S289V289LGtaTta11B.1.438.10.000107
S289V289IGtaAta11B.1.438.10.000107
S289V289LGtaCta11B.1.4970.000315
S289V289TGTaACa11B.1.4970.000315
S289V289VgtAgtG11B.1.5250.000113
S289V289IGtaAta11B.1.5750.000303
S289V289del1GtA-tT11B.1.5950.000261
S289V289GgTagGa11B.1.5960.000087
S289V289VgtAgtT11B.1.6090.000479
S289V289delGTA---11B.1.6090.000479
S289V289VgtAgtT11B.1.617.10.000129
S289V289delGTA---11B.1.617.10.000129
S289V289AgTagCa11B.1.617.20.000004
S289V289PGTACCG11B.1.617.20.000004
S289V289TGTaACa11B.1.617.20.000004
S289V289delGTA---11B.1.6200.000946
S289V289LGtaCta11B.1.6270.00202
S289V289VgtAgtG11B.1.6280.000352
S289V289delGTA---11B.1.6300.005236
S289V289IGtaAta11B.400.000364
S289V289IGtaAta11B.6.60.000889
S289V289VgtAgtG11C.10.002392
S289V289delGTA---11C.1.20.004255
S289V289VgtAgtG11C.110.010638
S289V289VgtAgtG11C.300.001727
S289V289IGtaAta11C.36.30.000567
S289V289LGtaTta11C.36.30.000567
S289V289VgtAgtG11D.20.000075
S289V289LGtaTta11D.20.000075
S289V289EgTagAa11D.20.000075
S289V289GgTagGa11D.20.000075
S289V289VgtAgtG11N.50.001767
S289V289del1GTA-NN11P.10.000016
S289V289IGtaAta11P.10.000016
S289V289IGtaAta11P.1.100.000269
S289V289IGtaAta11P.1.150.000232
S289V289LGtaTta11P.1.150.000232
S289V289VgtAgtG11P.1.90.004808
S289V289del1GtA-tN11Q.40.000455
S289V289AgTagCa11Q.80.000165

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.