CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 562

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
S562F562FsynttCttT1246312463123246-23248
S562F562deldelTTC---2626123246-23248
S562F562SnonsyntTctCc1111123246-23248
S562F562LnonsynttCttA850.62523246-23248
S562F562LnonsynTtcCtc830.37523246-23248
S562F562del1delttCtt-33123246-23248
S562F562VnonsynTtcGtc22123246-23248
S562F562CnonsyntTctGc11123246-23248
S562F562YnonsyntTctAc11123246-23248
S562F562PnonsynTTCCCA11123246-23248

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

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
S562F562FttCttT1246312463All0.002384
S562F562FttCttT38913891B.1.1.70.003483
S562F562FttCttT893893B.1.1.1530.978094
S562F562FttCttT842842B.10.007712
S562F562FttCttT781781B.1.1.1700.973815
S562F562FttCttT608608AY.40.000946
S562F562FttCttT541541B.1.10.009814
S562F562FttCttT497497B.1.617.20.001871
S562F562FttCttT450450B.1.1270.989011
S562F562FttCttT243243B.1.20.00214
S562F562FttCttT236236AY.440.001436
S562F562FttCttT213213AY.1030.001323
S562F562FttCttT192192AY.30.00191
S562F562FttCttT191191AY.250.001149
S562F562FttCttT150150P.10.002363
S562F562FttCttT129129B.1.3990.249516
S562F562FttCttT122122AY.430.000541
S562F562FttCttT119119B.1.9.40.730061
S562F562FttCttT107107AY.1200.003978
S562F562FttCttT8585B.1.1600.002651
S562F562FttCttT8181B.1.1770.001067
S562F562FttCttT7575B.1.4290.001765
S562F562FttCttT7070B.1.4270.003535
S562F562FttCttT6969B.1.177.810.013063
S562F562FttCttT6161AY.390.001507
S562F562FttCttT6060B.1.1.5190.002383
S562F562FttCttT5757AY.900.039014
S562F562FttCttT5656B.1.360.00817
S562F562FttCttT5555AY.1020.001458
S562F562FttCttT5353AD.20.011605
S562F562FttCttT5353AY.200.00206
S562F562FttCttT4848AY.420.001931
S562F562FttCttT4040AY.1190.001412
S562F562FttCttT3636AY.60.001481
S562F562FttCttT3636B.1.3510.00107
S562F562FttCttT3434B.1.2580.002263
S562F562FttCttT3333C.350.025542
S562F562FttCttT3232AY.4.20.000694
S562F562FttCttT3030B.1.5960.002614
S562F562FttCttT3030P.1.140.001434
S562F562FttCttT2929B.1.2210.00206
S562F562FttCttT2727B.1.5770.018557
S562F562delTTC---2626All0.000005
S562F562FttCttT2525B.1.5260.000588
S562F562FttCttT2424AY.3.10.002046
S562F562FttCttT2424B.1.1.4190.177778
S562F562FttCttT2323B.1.3690.00656
S562F562FttCttT2222AY.46.60.001589
S562F562FttCttT2121AY.330.001402
S562F562FttCttT2121AY.470.000653
S562F562FttCttT2121B.1.2430.001461
S562F562FttCttT2121Q.80.003463
S562F562FttCttT2020B.1.2410.016234
S562F562FttCttT1818B.1.2360.036961
S562F562FttCttT1717AY.290.000268
S562F562FttCttT1616AY.260.000453
S562F562FttCttT1515AY.50.00031
S562F562FttCttT1515AY.90.001014
S562F562FttCttT1515B.1.351.20.004539
S562F562FttCttT1414B.1.351.30.01227
S562F562FttCttT1313A.210.036011
S562F562FttCttT1313AE.80.006357
S562F562FttCttT1313B.1.177.860.002385
S562F562FttCttT1212AY.10.004749
S562F562FttCttT1212AY.230.000837
S562F562FttCttT1212AY.740.001388
S562F562FttCttT1212B.1.36.290.006208
S562F562StTctCc1111All0.000002
S562F562FttCttT1111AY.370.003477
S562F562FttCttT1111AY.39.10.000436
S562F562FttCttT1111AY.450.001339
S562F562FttCttT1111B.1.5950.002871
S562F562FttCttT1010AY.1000.00046
S562F562FttCttT1010B.1.1.280.003112
S562F562FttCttT1010B.1.1.3170.004117
S562F562FttCttT1010P.1.170.001618
S562F562FttCttT99B.1.1.1980.013216
S562F562FttCttT99C.370.001045
S562F562FttCttT99D.20.000675
S562F562LttCttA58All0.000001
S562F562LTtcCtc38All0.000001
S562F562FttCttT88AY.16.10.003759
S562F562FttCttT88AY.340.000776
S562F562FttCttT88AY.46.20.005083
S562F562FttCttT88AY.750.000448
S562F562FttCttT88B.1.4250.023952
S562F562FttCttT88C.160.008484
S562F562FttCttT77AY.1180.000439
S562F562delTTC---77AY.250.000042
S562F562FttCttT77AY.46.40.001152
S562F562FttCttT77AY.610.000733
S562F562FttCttT77B.1.1.3690.003124
S562F562FttCttT77B.1.177.210.000535
S562F562FttCttT77B.1.2100.014925
S562F562FttCttT77B.1.466.10.05036
S562F562FttCttT77P.1.150.001626
S562F562FttCttT66A.2.5.20.009434
S562F562FttCttT66AY.1130.000854
S562F562FttCttT66AY.1170.000507
S562F562FttCttT66AY.120.10.001926
S562F562FttCttT66AY.1210.000812
S562F562FttCttT66AY.590.003178
S562F562FttCttT66AY.9.20.00022
S562F562FttCttT66B0.000767
S562F562FttCttT66B.1.3190.018293
S562F562FttCttT66B.1.6370.000438
S562F562FttCttT66P.1.120.002904
S562F562FttCttT66P.20.00112
S562F562FttCttT55B.1.1.10.001633
S562F562FttCttT55B.1.1.2070.00591
S562F562FttCttT55B.1.1.2220.00102
S562F562FttCttT55B.1.177.540.003032
S562F562FttCttT55B.1.177.600.001092
S562F562FttCttT55B.1.438.10.000536
S562F562FttCttT55B.1.4660.116279
S562F562FttCttT55B.1.6210.000443
S562F562FttCttT55B.1.90.030864
S562F562FttCttT55P.1.160.001871
S562F562FttCttT55Q.10.000632
S562F562FttCttT44AY.1050.002572
S562F562FttCttT44AY.1090.002959
S562F562FttCttT44AY.140.000352
S562F562FttCttT44AY.29.10.000882
S562F562FttCttT44AY.980.000316
S562F562FttCttT44AY.98.10.000194
S562F562FttCttT44AY.99.20.000369
S562F562FttCttT44B.1.1.2140.000222
S562F562FttCttT44B.1.1.2160.003562
S562F562FttCttT44B.1.1.3060.001754
S562F562FttCttT44B.1.1.370.000771
S562F562FttCttT44B.1.1.3720.002755
S562F562delTTC---44B.1.1.70.000004
S562F562FttCttT44B.1.177.120.000607
S562F562FttCttT44B.1.2400.000862
S562F562FttCttT44B.1.2980.008457
S562F562FttCttT44B.1.9.50.022727
S562F562FttCttT44C.10.009569
S562F562FttCttT44R.10.00036
S562F562del1ttCtt-33All0.000001
S562F562FttCttT33AY.1160.00086
S562F562FttCttT33AY.460.000312
S562F562FttCttT33AY.46.50.000595
S562F562FttCttT33AY.5.40.00083
S562F562FttCttT33AY.720.004082
S562F562StTctCc33B.10.000027
S562F562FttCttT33B.1.1.3260.005282
S562F562FttCttT33B.1.1.330.001263
S562F562FttCttT33B.1.1.3480.002389
S562F562FttCttT33B.1.1.4090.008499
S562F562FttCttT33B.1.1.4340.001046
S562F562FttCttT33B.1.1.4480.006098
S562F562FttCttT33B.1.177.510.013699
S562F562FttCttT33B.1.1990.012397
S562F562FttCttT33B.1.214.20.001799
S562F562FttCttT33B.1.2340.000396
S562F562FttCttT33B.1.258.170.000312
S562F562FttCttT33B.1.3240.004815
S562F562FttCttT33B.1.4330.009585
S562F562FttCttT33B.1.4560.009804
S562F562FttCttT33B.1.4710.008197
S562F562FttCttT33B.1.617.10.000387
S562F562FttCttT33C.36.30.001702
S562F562FttCttT33C.40.03
S562F562FttCttT33Q.30.000435
S562F562FttCttT33Q.40.001364
S562F562FttCttT33Z.10.008671
S562F562VTtcGtc22All0
S562F562FttCttT22AY.130.000322
S562F562FttCttT22AY.320.001065
S562F562FttCttT22AY.360.000296
S562F562FttCttT22AY.4.40.000818
S562F562FttCttT22AY.4.50.000215
S562F562FttCttT22AY.400.001929
S562F562delTTC---22AY.430.000009
S562F562FttCttT22AY.550.001835
S562F562FttCttT22AY.680.000547
S562F562FttCttT22AY.70.000392
S562F562FttCttT22AY.7.10.000225
S562F562FttCttT22AY.700.000417
S562F562FttCttT22AY.850.000854
S562F562FttCttT22AY.9.10.000167
S562F562FttCttT22AY.9.2.10.003953
S562F562FttCttT22AY.920.000575
S562F562FttCttT22AY.990.002099
S562F562LTtcCtc12B.10.000009
S562F562LttCttA12B.10.000009
S562F562FttCttT22B.1.1.1710.007353
S562F562FttCttT22B.1.1.1760.000879
S562F562FttCttT22B.1.1.2300.018349
S562F562FttCttT22B.1.1.2840.000215
S562F562FttCttT22B.1.1.700.000682
S562F562FttCttT22B.1.1280.001271
S562F562FttCttT22B.1.177.350.001382
S562F562FttCttT22B.1.177.560.001335
S562F562FttCttT22B.1.3200.002491
S562F562FttCttT22B.1.36.170.000988
S562F562FttCttT22B.1.36.240.012346
S562F562FttCttT22B.1.36.310.003503
S562F562FttCttT22B.1.36.80.002
S562F562FttCttT22B.1.3610.002577
S562F562FttCttT22B.1.416.10.003125
S562F562FttCttT22B.1.4430.009346
S562F562FttCttT22B.1.5250.000226
S562F562FttCttT22B.1.5820.000981
S562F562FttCttT22B.1.5910.021277
S562F562FttCttT22B.1.6090.000959
S562F562FttCttT22P.1.10.000635
S562F562FttCttT22P.1.20.002312
S562F562FttCttT22P.1.70.000639
S562F562FttCttT22P.40.007605
S562F562FttCttT22W.40.002703
S562F562FttCttT11A.20.000662
S562F562StTctCc11A.50.001923
S562F562FttCttT11AA.10.007246
S562F562FttCttT11AB.10.008197
S562F562PTTCCCA11All0
S562F562YtTctAc11All0
S562F562CtTctGc11All0
S562F562FttCttT11AN.10.02
S562F562FttCttT11AS.20.015625
S562F562FttCttT11AU.10.001266
S562F562FttCttT11AY.1010.00049
S562F562FttCttT11AY.1040.001984
S562F562FttCttT11AY.1110.000183
S562F562FttCttT11AY.120.20.001285
S562F562FttCttT11AY.160.00038
S562F562FttCttT11AY.23.10.000417
S562F562FttCttT11AY.240.000431
S562F562FttCttT11AY.270.000065
S562F562FttCttT11AY.300.000396
S562F562FttCttT11AY.310.018519
S562F562FttCttT11AY.34.10.00051
S562F562FttCttT11AY.350.000233
S562F562delTTC---11AY.380.000499
S562F562FttCttT11AY.39.20.001541
S562F562delTTC---11AY.40.000002
S562F562FttCttT11AY.4.10.000737
S562F562StTctCc11AY.430.000004
S562F562delTTC---11AY.440.000006
S562F562del1ttCtt-11AY.440.000006
S562F562delTTC---11AY.46.40.000165
S562F562delTTC---11AY.46.60.000072
S562F562FttCttT11AY.480.000465
S562F562FttCttT11AY.490.003195
S562F562FttCttT11AY.510.000909
S562F562FttCttT11AY.530.000288
S562F562FttCttT11AY.540.000095
S562F562FttCttT11AY.560.001605
S562F562FttCttT11AY.570.000656
S562F562FttCttT11AY.630.000387
S562F562delTTC---11AY.750.000056
S562F562delTTC---11AY.75.10.00018
S562F562FttCttT11AY.75.10.00018
S562F562FttCttT11AY.780.001541
S562F562FttCttT11AY.790.001211
S562F562FttCttT11AY.810.001992
S562F562FttCttT11AY.840.000437
S562F562FttCttT11AY.870.000833
S562F562FttCttT11AY.880.000884
S562F562FttCttT11AY.910.00073
S562F562delTTC---11AY.990.001049
S562F562FttCttT11AZ.10.000867
S562F562PTTCCCA11B.10.000009
S562F562CtTctGc11B.10.000009
S562F562del1ttCtt-11B.10.000009
S562F562delTTC---11B.1.10.000018
S562F562FttCttT11B.1.1.1520.04
S562F562FttCttT11B.1.1.1940.00495
S562F562FttCttT11B.1.1.2200.001859
S562F562FttCttT11B.1.1.250.000569
S562F562FttCttT11B.1.1.2530.002506
S562F562FttCttT11B.1.1.2770.000759
S562F562FttCttT11B.1.1.2860.002899
S562F562FttCttT11B.1.1.2890.002083
S562F562FttCttT11B.1.1.290.010309
S562F562FttCttT11B.1.1.2910.000742
S562F562VTtcGtc11B.1.1.3000.010753
S562F562FttCttT11B.1.1.3110.000358
S562F562FttCttT11B.1.1.3340.016393
S562F562FttCttT11B.1.1.3510.002793
S562F562FttCttT11B.1.1.3520.03125
S562F562LTtcCtc11B.1.1.3770.001381
S562F562FttCttT11B.1.1.4130.006897
S562F562FttCttT11B.1.1.4320.001266
S562F562FttCttT11B.1.1.440.00241
S562F562FttCttT11B.1.1.480.002874
S562F562FttCttT11B.1.1.5250.005464
S562F562FttCttT11B.1.1.630.000386
S562F562LttCttA11B.1.1.70.000001
S562F562VTtcGtc11B.1.1.70.000001
S562F562FttCttT11B.1.110.30.000718
S562F562FttCttT11B.1.1110.001175
S562F562YtTctAc11B.1.1400.018868
S562F562FttCttT11B.1.1470.000756
S562F562StTctCc11B.1.1600.000031
S562F562LttCttA11B.1.1600.000031
S562F562FttCttT11B.1.1690.014925
S562F562FttCttT11B.1.177.320.00135
S562F562FttCttT11B.1.177.70.000165
S562F562FttCttT11B.1.177.730.000566
S562F562FttCttT11B.1.177.800.001912
S562F562FttCttT11B.1.177.820.000477
S562F562FttCttT11B.1.1950.005025
S562F562StTctCc11B.1.20.000009
S562F562LttCttA11B.1.20.000009
S562F562FttCttT11B.1.2220.001692
S562F562FttCttT11B.1.2320.000537
S562F562FttCttT11B.1.2350.002519
S562F562FttCttT11B.1.2390.001221
S562F562LttCttA11B.1.2430.00007
S562F562StTctCc11B.1.3250.006897
S562F562FttCttT11B.1.3290.000608
S562F562FttCttT11B.1.36.100.004785
S562F562FttCttT11B.1.36.160.001425
S562F562FttCttT11B.1.36.180.00042
S562F562FttCttT11B.1.36.190.009259
S562F562del1ttCtt-11B.1.36.290.000517
S562F562FttCttT11B.1.36.370.002778
S562F562FttCttT11B.1.3670.000792
S562F562StTctCc11B.1.3690.000285
S562F562FttCttT11B.1.3710.001122
S562F562FttCttT11B.1.3750.00082
S562F562FttCttT11B.1.3950.007042
S562F562FttCttT11B.1.4000.000429
S562F562FttCttT11B.1.4040.001302
S562F562FttCttT11B.1.4110.003704
S562F562delTTC---11B.1.4150.014286
S562F562FttCttT11B.1.4420.035714
S562F562FttCttT11B.1.466.20.000391
S562F562FttCttT11B.1.4680.005714
S562F562FttCttT11B.1.4700.001404
S562F562FttCttT11B.1.4740.001901
S562F562FttCttT11B.1.4970.000315
S562F562FttCttT11B.1.5450.014493
S562F562FttCttT11B.1.5600.00463
S562F562FttCttT11B.1.5630.016949
S562F562FttCttT11B.1.5670.003333
S562F562FttCttT11B.1.5750.000303
S562F562FttCttT11B.1.5760.000907
S562F562StTctCc11B.1.5990.00365
S562F562FttCttT11B.1.5990.00365
S562F562delTTC---11B.1.617.20.000004
S562F562delTTC---11B.1.6200.000946
S562F562FttCttT11B.1.6200.000946
S562F562FttCttT11B.1.6230.000536
S562F562FttCttT11B.1.6250.002353
S562F562FttCttT11B.1.6270.00202
S562F562FttCttT11B.1.6330.041667
S562F562FttCttT11B.1.690.035714
S562F562FttCttT11B.40.002208
S562F562FttCttT11B.450.003831
S562F562FttCttT11B.6.10.026316
S562F562FttCttT11C.110.010638
S562F562FttCttT11C.310.017857
S562F562FttCttT11C.360.000911
S562F562FttCttT11C.36.3.10.002717
S562F562StTctCc11D.20.000075
S562F562LTtcCtc11D.20.000075
S562F562FttCttT11N.60.007092
S562F562FttCttT11P.1.100.000269
S562F562FttCttT11P.1.60.001946
S562F562FttCttT11P.70.004367
S562F562delTTC---11Q.20.000613
S562F562FttCttT11Q.70.001111

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.