CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 673

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
S673S673TnonsynaGtaCt201920170.99900923579-23581
S673S673TnonsynaGTaCG201920.00099058923579-23581
S673S673SsynagTagC147147123579-23581
S673S673GnonsynAgtGgt1071050.98130823579-23581
S673S673GnonsynAgTGgA10720.018691623579-23581
S673S673deldelAGT---9696123579-23581
S673S673InonsynaGtaTt8585123579-23581
S673S673RnonsynagTagG34190.55882423579-23581
S673S673RnonsynAgtCgt34100.29411823579-23581
S673S673RnonsynagTagA3430.088235323579-23581
S673S673RnonsynAgTCgA3420.058823523579-23581
S673S673del2delAGt--t99123579-23581
S673S673del1delAgt-gt640.66666723579-23581
S673S673del1delAgT-gC610.16666723579-23581
S673S673del1delagTag-610.16666723579-23581
S673S673CnonsynAgtTgt33123579-23581
S673S673NnonsynaGtaAt33123579-23581
S673S673KnonsynaGTaAG22123579-23581
S673S673LnonsynAGtCTt22123579-23581
S673S673YnonsynAGtTAt11123579-23581
S673S673DnonsynAGtGAt11123579-23581

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

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
S673S673TaGtaCt20172019All0.000386
S673S673TaGTaCG22019All0
S673S673TaGtaCt697697B.1.1.4330.992877
S673S673TaGtaCt623623B.1.1.390.317533
S673S673TaGtaCt154154AY.440.000937
S673S673SagTagC147147All0.000028
S673S673GAgtGgt105107All0.00002
S673S673GAgTGgA2107All0
S673S673TaGtaCt9898B.1.1770.00129
S673S673delAGT---9696All0.000018
S673S673IaGtaTt8585All0.000016
S673S673TaGtaCt6666B.10.000605
S673S673GAgtGgt5757B.1.258.110.022592
S673S673TaGtaCt4242B.1.617.20.000158
S673S673SagTagC3838B.1.4270.001919
S673S673RagTagG1934All0.000004
S673S673RAgtCgt1034All0.000002
S673S673RagTagA334All0.000001
S673S673RAgTCgA234All0
S673S673TaGtaCt3232B.1.1.70.000029
S673S673TaGtaCt3232B.1.1600.000998
S673S673TaGtaCt2323B.1.1.2770.017451
S673S673TaGtaCt2323B.1.36.310.04028
S673S673TaGtaCt2222AY.1030.000137
S673S673SagTagC2222AY.140.001936
S673S673TaGtaCt1919B.1.1.4340.006623
S673S673TaGtaCt1818B.1.10.000327
S673S673delAGT---1717B.10.000156
S673S673IaGtaTt1515P.10.000236
S673S673TaGtaCt1313AY.40.00002
S673S673TaGtaCt1313B.1.1.2220.002652
S673S673SagTagC1313B.1.160.260.031477
S673S673TaGtaCt1313B.1.160.320.055794
S673S673TaGtaCt1212AY.430.000053
S673S673SagTagC1111AY.440.000067
S673S673IaGtaTt1010B.1.1.70.000009
S673S673GAgtGgt1010B.1.617.20.000038
S673S673del2AGt--t99All0.000002
S673S673TaGtaCt99AY.1020.000239
S673S673IaGtaTt99AY.40.000014
S673S673SagTagC99B.1.1.70.000008
S673S673TaGtaCt99B.1.5260.000212
S673S673SagTagC77AY.250.000042
S673S673SagTagC77B.1.1.3160.006475
S673S673delAGT---77B.1.1.70.000006
S673S673del1Agt-gt46All0.000001
S673S673del1AgT-gC16All0
S673S673del1agTag-16All0
S673S673SagTagC66AY.1030.000037
S673S673GAgtGgt66AY.1130.000854
S673S673TaGtaCt66AY.1190.000212
S673S673delAGT---66AY.430.000027
S673S673delAGT---66B.1.20.000053
S673S673SagTagC66B.1.20.000053
S673S673delAGT---66P.10.000095
S673S673TaGtaCt55AY.34.10.00255
S673S673TaGtaCt55AY.390.000124
S673S673IaGtaTt55B.1.1.390.002548
S673S673RAgtCgt45B.1.1.70.000004
S673S673RagTagG15B.1.1.70.000001
S673S673IaGtaTt55B.1.177.600.001092
S673S673RagTagG55B.1.177.810.000947
S673S673RagTagG240.111111
S673S673TaGTaCG240.111111
S673S673TaGtaCt240.111111
S673S673RAgTCgA240.111111
S673S673IaGtaTt44AY.1030.000025
S673S673TaGtaCt44AY.30.00004
S673S673TaGtaCt44AY.3.10.000341
S673S673TaGtaCt44AY.330.000267
S673S673SagTagC44AY.40.000006
S673S673GAgtGgt44B.1.1770.000053
S673S673TaGtaCt44B.1.177.210.000306
S673S673TaGtaCt44B.1.5090.003463
S673S673IaGtaTt44B.1.5260.000094
S673S673RAgtCgt24B.1.617.20.000008
S673S673RagTagG14B.1.617.20.000004
S673S673RagTagA14B.1.617.20.000004
S673S673CAgtTgt33All0.000001
S673S673NaGtaAt33All0.000001
S673S673TaGtaCt33AY.200.000117
S673S673delAGT---33AY.250.000018
S673S673GAgtGgt33B.10.000027
S673S673IaGtaTt33B.10.000027
S673S673GAgtGgt33B.1.1.70.000003
S673S673delAGT---33B.1.1600.000094
S673S673SagTagC33B.1.1770.00004
S673S673RagTagG33B.1.2400.000647
S673S673TaGtaCt33B.1.4990.003151
S673S673delAGT---33B.1.617.20.000011
S673S673delAGT---33B.1.6210.000266
S673S673IaGtaTt33D.20.000225
S673S673SagTagC33P.10.000047
S673S673IaGtaTt33P.1.140.000143
S673S673delAGT---33P.1.150.000697
S673S673del1Agt-gt220.111111
S673S673KaGTaAG220.111111
S673S673IaGtaTt22A.2.50.000998
S673S673KaGTaAG22All0
S673S673LAGtCTt22All0
S673S673SagTagC22AY.1070.000932
S673S673TaGtaCt22AY.250.000012
S673S673TaGtaCt22AY.290.000032
S673S673TaGtaCt22AY.350.000466
S673S673GAgtGgt22AY.40.000003
S673S673TaGtaCt22AY.4.20.000043
S673S673GAgtGgt22AY.440.000012
S673S673GAgtGgt22AY.470.000062
S673S673TaGtaCt22AY.710.00095
S673S673IaGtaTt22AY.98.10.000097
S673S673RAgtCgt22B.10.000018
S673S673SagTagC22B.10.000018
S673S673SagTagC22B.1.10.000036
S673S673delAGT---22B.1.10.000036
S673S673GAgTGgA12B.1.10.000018
S673S673GAgtGgt12B.1.10.000018
S673S673TaGtaCt22B.1.1.3060.000877
S673S673NaGtaAt22B.1.1.70.000002
S673S673IaGtaTt22B.1.1770.000026
S673S673delAGT---22B.1.1770.000026
S673S673del2AGt--t22B.1.1770.000026
S673S673IaGtaTt22B.1.20.000018
S673S673TaGtaCt22B.1.2210.000142
S673S673TaGtaCt22B.1.2580.000133
S673S673GAgtGgt22B.1.5260.000047
S673S673TaGtaCt22B.1.5600.009259
S673S673delAGT---22B.1.5640.000852
S673S673delAGT---22B.1.5960.000174
S673S673IaGtaTt22B.1.617.20.000008
S673S673SagTagC22B.1.617.20.000008
S673S673delAGT---22P.1.10.000635
S673S673GAgtGgt22P.1.10.000635
S673S673TaGtaCt11A0.000387
S673S673delAGT---11A.20.000662
S673S673delAGT---11A.2.20.001689
S673S673SagTagC11A.2.50.000499
S673S673TaGtaCt11AB.10.008197
S673S673DAGtGAt11All0
S673S673YAGtTAt11All0
S673S673GAgtGgt11AU.20.002421
S673S673GAgtGgt11AY.1020.000027
S673S673delAGT---11AY.1030.000006
S673S673RagTagG11AY.1060.000335
S673S673TaGtaCt11AY.1160.000287
S673S673del1agTag-11AY.1160.000287
S673S673RagTagG11AY.1170.000085
S673S673TaGtaCt11AY.1180.000063
S673S673GAgtGgt11AY.1190.000035
S673S673SagTagC11AY.1200.000037
S673S673TaGtaCt11AY.1200.000037
S673S673TaGtaCt11AY.16.10.00047
S673S673TaGtaCt11AY.230.00007
S673S673GAgtGgt11AY.250.000006
S673S673IaGtaTt11AY.250.000006
S673S673CAgtTgt11AY.250.000006
S673S673TaGtaCt11AY.260.000028
S673S673GAgtGgt11AY.290.000016
S673S673delAGT---11AY.290.000016
S673S673RAgtCgt11AY.290.000016
S673S673del1AgT-gC11AY.30.00001
S673S673IaGtaTt11AY.30.00001
S673S673GAgtGgt11AY.320.000532
S673S673SagTagC11AY.380.000499
S673S673SagTagC11AY.390.000025
S673S673RAgtCgt11AY.40.000002
S673S673SagTagC11AY.4.2.10.000149
S673S673IaGtaTt11AY.4.40.000409
S673S673RagTagG11AY.4.40.000409
S673S673TaGtaCt11AY.420.00004
S673S673SagTagC11AY.430.000004
S673S673IaGtaTt11AY.440.000006
S673S673RagTagG11AY.440.000006
S673S673DAGtGAt11AY.440.000006
S673S673IaGtaTt11AY.450.000122
S673S673TaGtaCt11AY.470.000031
S673S673IaGtaTt11AY.470.000031
S673S673GAgTGgA11AY.480.000465
S673S673IaGtaTt11AY.50.000021
S673S673RagTagG11AY.60.000041
S673S673LAGtCTt11AY.670.000464
S673S673TaGtaCt11AY.7.10.000113
S673S673TaGtaCt11AY.740.000116
S673S673delAGT---11AY.840.000437
S673S673CAgtTgt11AY.90.000068
S673S673TaGtaCt11AY.9.20.000037
S673S673delAGT---11AY.9.20.000037
S673S673TaGtaCt11AY.920.000287
S673S673TaGtaCt11AY.930.000273
S673S673delAGT---11AY.990.001049
S673S673TaGtaCt11AY.99.20.000092
S673S673del2AGt--t11B.10.000009
S673S673del1Agt-gt11B.10.000009
S673S673del1Agt-gt11B.1.10.000018
S673S673YAGtTAt11B.1.10.000018
S673S673CAgtTgt11B.1.10.000018
S673S673NaGtaAt11B.1.10.000018
S673S673IaGtaTt11B.1.1.1640.005155
S673S673IaGtaTt11B.1.1.2200.001859
S673S673delAGT---11B.1.1.2220.000204
S673S673TaGtaCt11B.1.1.280.000311
S673S673IaGtaTt11B.1.1.2980.000862
S673S673TaGtaCt11B.1.1.3110.000358
S673S673TaGtaCt11B.1.1.3170.000412
S673S673SagTagC11B.1.1.3370.003597
S673S673delAGT---11B.1.1.3720.000689
S673S673delAGT---11B.1.1.390.00051
S673S673TaGtaCt11B.1.1.470.005348
S673S673TaGtaCt11B.1.1.5190.00004
S673S673TaGtaCt11B.1.1.700.000341
S673S673delAGT---11B.1.1.700.000341
S673S673RagTagA11B.1.1600.000031
S673S673delAGT---11B.1.160.160.000929
S673S673TaGtaCt11B.1.160.300.002976
S673S673delAGT---11B.1.160.330.004425
S673S673IaGtaTt11B.1.160.80.001289
S673S673delAGT---11B.1.177.120.000152
S673S673TaGtaCt11B.1.177.120.000152
S673S673TaGtaCt11B.1.177.170.000821
S673S673IaGtaTt11B.1.177.190.001431
S673S673del2AGt--t11B.1.177.210.000076
S673S673delAGT---11B.1.177.210.000076
S673S673TaGtaCt11B.1.177.230.003236
S673S673del2AGt--t11B.1.177.350.000691
S673S673RagTagG11B.1.177.440.000519
S673S673RagTagG11B.1.177.500.004695
S673S673TaGtaCt11B.1.177.690.001484
S673S673GAgtGgt11B.1.20.000009
S673S673del2AGt--t11B.1.20.000009
S673S673TaGtaCt11B.1.20.000009
S673S673LAGtCTt11B.1.20.000009
S673S673delAGT---11B.1.2210.000071
S673S673GAgtGgt11B.1.2210.000071
S673S673delAGT---11B.1.2340.000132
S673S673TaGtaCt11B.1.2430.00007
S673S673TaGtaCt11B.1.258.110.000396
S673S673delAGT---11B.1.258.220.002667
S673S673GAgtGgt11B.1.3240.001605
S673S673delAGT---11B.1.3250.006897
S673S673TaGtaCt11B.1.3320.003497
S673S673TaGtaCt11B.1.360.000146
S673S673SagTagC11B.1.360.000146
S673S673del2AGt--t11B.1.3710.001122
S673S673delAGT---11B.1.390.003906
S673S673delAGT---11B.1.4290.000024
S673S673TaGtaCt11B.1.4290.000024
S673S673delAGT---11B.1.4500.011364
S673S673TaGtaCt11B.1.466.20.000391
S673S673delAGT---11B.1.4970.000315
S673S673TaGtaCt11B.1.5250.000113
S673S673delAGT---11B.1.5800.004065
S673S673GAgtGgt11B.1.5950.000261
S673S673del2AGt--t11B.1.5950.000261
S673S673TaGtaCt11B.1.5960.000087
S673S673delAGT---11B.1.6200.000946
S673S673RagTagA11B.1.6200.000946
S673S673SagTagC11B.1.621.10.000506
S673S673delAGT---11B.1.6270.00202
S673S673delAGT---11B.1.6380.052632
S673S673TaGtaCt11B.400.000364
S673S673GAgtGgt11C.350.000774
S673S673del2AGt--t11C.36.30.000567
S673S673IaGtaTt11C.36.3.10.002717
S673S673delAGT---11C.370.000116
S673S673SagTagC11C.370.000116
S673S673delAGT---11P.1.130.000898
S673S673IaGtaTt11P.1.170.000162

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.