CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 1239

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
S1239S1239SsynagTagC24882488125277-25279
S1239S1239TnonsynaGtaCt2282270.99561425277-25279
S1239S1239TnonsynaGTaCC22810.0043859625277-25279
S1239S1239deldelAGT---124124125277-25279
S1239S1239GnonsynAgtGgt9393125277-25279
S1239S1239NnonsynaGtaAt8585125277-25279
S1239S1239InonsynaGtaTt6666125277-25279
S1239S1239RnonsynagTagG60480.825277-25279
S1239S1239RnonsynAgtCgt6070.11666725277-25279
S1239S1239RnonsynagTagA6050.083333325277-25279
S1239S1239CnonsynAgtTgt2828125277-25279
S1239S1239del1delagTag-1060.625277-25279
S1239S1239del1delAgt-gt1040.425277-25279
S1239S1239del2delAGt--t33125277-25279
S1239S1239PnonsynAGtCCt22125277-25279
S1239S1239HnonsynAGtCAt22125277-25279
S1239S1239KnonsynaGTaAA210.525277-25279
S1239S1239KnonsynaGTaAG210.525277-25279
S1239S1239DnonsynAGtGAt11125277-25279
S1239S1239FnonsynAGtTTt11125277-25279

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

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
S1239S1239SagTagC24882488All0.000476
S1239S1239SagTagC21052105AY.140.185267
S1239S1239TaGtaCt227228All0.000043
S1239S1239TaGTaCC1228All0
S1239S1239delAGT---124124All0.000024
S1239S1239GAgtGgt9393All0.000018
S1239S1239NaGtaAt8585All0.000016
S1239S1239TaGtaCt7575B.1.1.70.000067
S1239S1239IaGtaTt6666All0.000013
S1239S1239RagTagG4860All0.000009
S1239S1239RAgtCgt760All0.000001
S1239S1239RagTagA560All0.000001
S1239S1239delAGT---4949B.1.1.70.000044
S1239S1239SagTagC4444B.1.617.20.000166
S1239S1239SagTagC3333AY.190.037628
S1239S1239SagTagC3030AY.540.00286
S1239S1239CAgtTgt2828All0.000005
S1239S1239TaGtaCt2727P.1.140.001291
S1239S1239SagTagC2424B.1.5750.007282
S1239S1239SagTagC2121AY.40.000033
S1239S1239SagTagC2020AY.380.009985
S1239S1239TaGtaCt2020B.1.20.000176
S1239S1239SagTagC1818AY.440.00011
S1239S1239GAgtGgt1717P.10.000268
S1239S1239delAGT---1616AY.4.50.00172
S1239S1239SagTagC1515AY.640.008929
S1239S1239NaGtaAt1414AY.390.000346
S1239S1239NaGtaAt1414B.1.1.70.000013
S1239S1239SagTagC1313AY.980.001027
S1239S1239SagTagC1212AY.130.001932
S1239S1239GAgtGgt1212AY.460.001249
S1239S1239SagTagC1212AY.780.01849
S1239S1239SagTagC1212B.1.1.4300.5
S1239S1239IaGtaTt1212B.1.1.70.000011
S1239S1239GAgtGgt1212B.1.20.000106
S1239S1239delAGT---1111B.1.1770.000145
S1239S1239del1agTag-610All0.000001
S1239S1239del1Agt-gt410All0.000001
S1239S1239SagTagC1010B.1.1.5190.000397
S1239S1239IaGtaTt99AY.40.000014
S1239S1239SagTagC99B.1.20.000079
S1239S1239TaGtaCt88AY.340.000776
S1239S1239TaGtaCt88AY.40.000012
S1239S1239TaGtaCt88B.1.1.2770.00607
S1239S1239SagTagC88B.1.1.70.000007
S1239S1239TaGtaCt88B.1.617.20.00003
S1239S1239GAgtGgt88B.1.6370.000585
S1239S1239RagTagG77AY.10.00277
S1239S1239RagTagG77AY.140.000616
S1239S1239SagTagC77AY.430.000031
S1239S1239TaGtaCt77AY.540.000667
S1239S1239CAgtTgt77B.1.1.70.000006
S1239S1239SagTagC66AY.680.001642
S1239S1239SagTagC66AY.75.10.001082
S1239S1239SagTagC66B.10.000055
S1239S1239GAgtGgt66B.1.1.70.000005
S1239S1239IaGtaTt66B.1.617.20.000023
S1239S1239SagTagC66P.1.20.006936
S1239S1239TaGtaCt55AY.1190.000177
S1239S1239RagTagG55AY.250.00003
S1239S1239NaGtaAt55AY.260.000142
S1239S1239CAgtTgt55AY.40.000008
S1239S1239GAgtGgt55AY.40.000008
S1239S1239SagTagC55AY.620.002179
S1239S1239NaGtaAt55B.10.000046
S1239S1239TaGtaCt55B.1.10.000091
S1239S1239TaGtaCt55B.1.5960.000436
S1239S1239delAGT---55B.1.617.20.000019
S1239S1239RagTagG34AY.1030.000019
S1239S1239RAgtCgt14AY.1030.000006
S1239S1239SagTagC44AY.1190.000141
S1239S1239delAGT---44AY.40.000006
S1239S1239TaGtaCt44AY.430.000018
S1239S1239NaGtaAt44AY.530.00115
S1239S1239SagTagC44B.1.1.390.002039
S1239S1239TaGtaCt44B.1.177.210.000306
S1239S1239NaGtaAt44B.1.6210.000354
S1239S1239del2AGt--t33All0.000001
S1239S1239TaGtaCt33AY.1020.00008
S1239S1239SagTagC33AY.1030.000019
S1239S1239NaGtaAt33AY.1090.002219
S1239S1239RagTagG33AY.200.000117
S1239S1239TaGtaCt33AY.230.000209
S1239S1239NaGtaAt33AY.250.000018
S1239S1239SagTagC33AY.260.000085
S1239S1239RagTagG23AY.260.000057
S1239S1239RagTagA13AY.260.000028
S1239S1239NaGtaAt33AY.290.000047
S1239S1239delAGT---33AY.30.00003
S1239S1239CAgtTgt33AY.430.000013
S1239S1239GAgtGgt33AY.440.000018
S1239S1239RagTagG33AY.440.000018
S1239S1239NaGtaAt33AY.50.000062
S1239S1239SagTagC33AY.590.001589
S1239S1239SagTagC33AY.750.000168
S1239S1239SagTagC33AY.870.002498
S1239S1239IaGtaTt33B.10.000027
S1239S1239del1agTag-23B.10.000018
S1239S1239del1Agt-gt13B.10.000009
S1239S1239IaGtaTt33B.1.10.000054
S1239S1239IaGtaTt33B.1.1.1150.026786
S1239S1239del1agTag-23B.1.1770.000026
S1239S1239del1Agt-gt13B.1.1770.000013
S1239S1239GAgtGgt33B.1.4270.000151
S1239S1239IaGtaTt33D.20.000225
S1239S1239NaGtaAt33L.30.010638
S1239S1239PAGtCCt22All0
S1239S1239HAGtCAt22All0
S1239S1239KaGTaAA12All0
S1239S1239KaGTaAG12All0
S1239S1239RagTagG22AY.1000.000092
S1239S1239SagTagC22AY.1020.000053
S1239S1239IaGtaTt22AY.1030.000012
S1239S1239TaGtaCt22AY.1060.00067
S1239S1239SagTagC22AY.1200.000074
S1239S1239delAGT---22AY.1200.000074
S1239S1239GAgtGgt22AY.140.000176
S1239S1239GAgtGgt22AY.250.000012
S1239S1239delAGT---22AY.250.000012
S1239S1239TaGtaCt22AY.250.000012
S1239S1239TaGtaCt22AY.30.00002
S1239S1239NaGtaAt22AY.30.00002
S1239S1239SagTagC22AY.30.00002
S1239S1239RagTagG12AY.30.00001
S1239S1239RAgtCgt12AY.30.00001
S1239S1239RagTagG22AY.430.000009
S1239S1239NaGtaAt22AY.430.000009
S1239S1239IaGtaTt22AY.440.000012
S1239S1239TaGtaCt22AY.440.000012
S1239S1239SagTagC22AY.460.000208
S1239S1239RagTagG22AY.470.000062
S1239S1239SagTagC22AY.470.000062
S1239S1239SagTagC22AY.650.001066
S1239S1239TaGtaCt22B.10.000018
S1239S1239GAgtGgt22B.10.000018
S1239S1239RAgtCgt12B.10.000009
S1239S1239RagTagA12B.10.000009
S1239S1239delAGT---22B.1.10.000036
S1239S1239SagTagC22B.1.10.000036
S1239S1239NaGtaAt22B.1.1.10.000653
S1239S1239delAGT---22B.1.1.370.000386
S1239S1239del1agTag-12B.1.1.70.000001
S1239S1239del1Agt-gt12B.1.1.70.000001
S1239S1239delAGT---22B.1.1600.000062
S1239S1239GAgtGgt22B.1.177.380.020833
S1239S1239delAGT---22B.1.177.40.000422
S1239S1239NaGtaAt22B.1.20.000018
S1239S1239TaGtaCt22B.1.3510.000059
S1239S1239GAgtGgt22B.1.3510.000059
S1239S1239GAgtGgt22B.1.360.000292
S1239S1239TaGtaCt22B.1.4280.002041
S1239S1239IaGtaTt22B.1.4290.000047
S1239S1239GAgtGgt22B.1.596.10.018692
S1239S1239NaGtaAt22B.1.617.20.000008
S1239S1239IaGtaTt22P.10.000032
S1239S1239delAGT---22P.1.150.000465
S1239S1239SagTagC22P.20.000373
S1239S1239TaGtaCt22P.70.008734
S1239S1239SagTagC11A0.000387
S1239S1239IaGtaTt11A.240.071429
S1239S1239SagTagC11A.270.001656
S1239S1239FAGtTTt11All0
S1239S1239DAGtGAt11All0
S1239S1239NaGtaAt11AY.1000.000046
S1239S1239RagTagG11AY.1020.000027
S1239S1239GAgtGgt11AY.1020.000027
S1239S1239NaGtaAt11AY.1020.000027
S1239S1239GAgtGgt11AY.1030.000006
S1239S1239NaGtaAt11AY.1040.001984
S1239S1239RagTagG11AY.1130.000142
S1239S1239TaGtaCt11AY.1160.000287
S1239S1239SagTagC11AY.1170.000085
S1239S1239IaGtaTt11AY.1180.000063
S1239S1239RagTagG11AY.1190.000035
S1239S1239HAGtCAt11AY.1200.000037
S1239S1239SagTagC11AY.1210.000135
S1239S1239RagTagG11AY.130.000161
S1239S1239SagTagC11AY.160.00038
S1239S1239TaGtaCt11AY.16.10.00047
S1239S1239RagTagG11AY.190.00114
S1239S1239TaGtaCt11AY.20.000356
S1239S1239SagTagC11AY.200.000039
S1239S1239SagTagC11AY.230.00007
S1239S1239NaGtaAt11AY.230.00007
S1239S1239delAGT---11AY.230.00007
S1239S1239GAgtGgt11AY.230.00007
S1239S1239del2AGt--t11AY.240.000431
S1239S1239TaGtaCt11AY.260.000028
S1239S1239TaGtaCt11AY.270.000065
S1239S1239IaGtaTt11AY.290.000016
S1239S1239GAgtGgt11AY.290.000016
S1239S1239TaGtaCt11AY.290.000016
S1239S1239SagTagC11AY.290.000016
S1239S1239GAgtGgt11AY.30.00001
S1239S1239SagTagC11AY.300.000396
S1239S1239SagTagC11AY.320.000532
S1239S1239SagTagC11AY.340.000097
S1239S1239NaGtaAt11AY.350.000233
S1239S1239SagTagC11AY.390.000025
S1239S1239NaGtaAt11AY.39.10.00004
S1239S1239del2AGt--t11AY.40.000002
S1239S1239del1Agt-gt11AY.40.000002
S1239S1239TaGtaCt11AY.4.30.000842
S1239S1239CAgtTgt11AY.420.00004
S1239S1239HAGtCAt11AY.430.000004
S1239S1239IaGtaTt11AY.430.000004
S1239S1239TaGtaCt11AY.460.000104
S1239S1239TaGtaCt11AY.46.10.001027
S1239S1239NaGtaAt11AY.470.000031
S1239S1239IaGtaTt11AY.470.000031
S1239S1239NaGtaAt11AY.480.000465
S1239S1239SagTagC11AY.490.003195
S1239S1239SagTagC11AY.50.000021
S1239S1239delAGT---11AY.50.000021
S1239S1239SagTagC11AY.500.000799
S1239S1239SagTagC11AY.510.000909
S1239S1239delAGT---11AY.60.000041
S1239S1239RagTagG11AY.670.000464
S1239S1239TaGtaCt11AY.670.000464
S1239S1239delAGT---11AY.680.000274
S1239S1239GAgtGgt11AY.70.000196
S1239S1239SagTagC11AY.70.000196
S1239S1239SagTagC11AY.720.001361
S1239S1239RagTagG11AY.750.000056
S1239S1239NaGtaAt11AY.750.000056
S1239S1239CAgtTgt11AY.80.000606
S1239S1239delAGT---11AY.810.001992
S1239S1239RagTagG11AY.850.000427
S1239S1239SagTagC11AY.860.00083
S1239S1239CAgtTgt11AY.9.10.000084
S1239S1239SagTagC11AY.9.20.000037
S1239S1239IaGtaTt11AY.910.00073
S1239S1239IaGtaTt11AY.980.000079
S1239S1239CAgtTgt11AY.980.000079
S1239S1239TaGtaCt11AY.99.20.000092
S1239S1239KaGTaAA11B.10.000009
S1239S1239delAGT---11B.10.000009
S1239S1239DAGtGAt11B.10.000009
S1239S1239CAgtTgt11B.1.10.000018
S1239S1239GAgtGgt11B.1.10.000018
S1239S1239IaGtaTt11B.1.1.1760.000439
S1239S1239GAgtGgt11B.1.1.2160.00089
S1239S1239TaGtaCt11B.1.1.250.000569
S1239S1239SagTagC11B.1.1.250.000569
S1239S1239CAgtTgt11B.1.1.2570.009709
S1239S1239IaGtaTt11B.1.1.3060.000438
S1239S1239RagTagA11B.1.1.3110.000358
S1239S1239TaGtaCt11B.1.1.3690.000446
S1239S1239IaGtaTt11B.1.1.390.00051
S1239S1239GAgtGgt11B.1.1.500.000679
S1239S1239TaGTaCC11B.1.1.5230.001563
S1239S1239RAgtCgt11B.1.1.70.000001
S1239S1239PAGtCCt11B.1.1.70.000001
S1239S1239TaGtaCt11B.1.1.700.000341
S1239S1239TaGtaCt11B.1.110.30.000718
S1239S1239NaGtaAt11B.1.110.30.000718
S1239S1239IaGtaTt11B.1.110.30.000718
S1239S1239RagTagA11B.1.1600.000031
S1239S1239IaGtaTt11B.1.1600.000031
S1239S1239CAgtTgt11B.1.160.140.002119
S1239S1239delAGT---11B.1.160.230.004831
S1239S1239TaGtaCt11B.1.1770.000013
S1239S1239IaGtaTt11B.1.1770.000013
S1239S1239delAGT---11B.1.177.100.000878
S1239S1239delAGT---11B.1.177.170.000821
S1239S1239delAGT---11B.1.177.180.00116
S1239S1239delAGT---11B.1.177.190.001431
S1239S1239GAgtGgt11B.1.177.210.000076
S1239S1239RagTagG11B.1.177.40.000211
S1239S1239delAGT---11B.1.177.540.000606
S1239S1239TaGtaCt11B.1.177.70.000165
S1239S1239delAGT---11B.1.177.760.002494
S1239S1239FAGtTTt11B.1.177.810.000189
S1239S1239CAgtTgt11B.1.177.90.001332
S1239S1239delAGT---11B.1.221.10.002907
S1239S1239IaGtaTt11B.1.2230.002778
S1239S1239delAGT---11B.1.230.006061
S1239S1239RAgtCgt11B.1.2330.014085
S1239S1239RagTagA11B.1.2360.002053
S1239S1239SagTagC11B.1.2430.00007
S1239S1239IaGtaTt11B.1.3130.006579
S1239S1239RagTagG11B.1.3320.003497
S1239S1239PAGtCCt11B.1.3510.00003
S1239S1239CAgtTgt11B.1.3510.00003
S1239S1239NaGtaAt11B.1.3510.00003
S1239S1239SagTagC11B.1.3550.011111
S1239S1239RagTagG11B.1.360.000146
S1239S1239delAGT---11B.1.36.170.000494
S1239S1239delAGT---11B.1.36.180.00042
S1239S1239delAGT---11B.1.3890.001002
S1239S1239TaGtaCt11B.1.3980.002976
S1239S1239IaGtaTt11B.1.4080.00369
S1239S1239delAGT---11B.1.4090.000781
S1239S1239IaGtaTt11B.1.4270.00005
S1239S1239del2AGt--t11B.1.4290.000024
S1239S1239GAgtGgt11B.1.4290.000024
S1239S1239IaGtaTt11B.1.438.10.000107
S1239S1239SagTagC11B.1.5180.011765
S1239S1239IaGtaTt11B.1.5260.000024
S1239S1239RAgtCgt11B.1.5260.000024
S1239S1239GAgtGgt11B.1.6060.006024
S1239S1239del1agTag-11B.1.617.10.000129
S1239S1239KaGTaAG11B.1.617.20.000004
S1239S1239CAgtTgt11B.1.617.20.000004
S1239S1239SagTagC11B.1.6300.005236
S1239S1239RAgtCgt11B.1.6370.000073
S1239S1239delAGT---11C.170.055556
S1239S1239SagTagC11C.370.000116
S1239S1239SagTagC11D.20.000075
S1239S1239CAgtTgt11D.20.000075
S1239S1239NaGtaAt11N.90.005952
S1239S1239TaGtaCt11P.10.000016
S1239S1239delAGT---11P.10.000016
S1239S1239CAgtTgt11P.1.10.000318
S1239S1239GAgtGgt11P.1.120.000484
S1239S1239CAgtTgt11P.1.140.000048
S1239S1239TaGtaCt11P.1.170.000162
S1239S1239NaGtaAt11P.1.80.004785
S1239S1239TaGtaCt11Q.80.000165
S1239S1239NaGtaAt11R.10.00009
S1239S1239delAGT---11U.30.003861

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.