CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp6 : CodonNum = 104

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/nsp6104S104delS3673deldelAGT---13881388111282-11284
ORF1ab/nsp6104S104NS3673NnonsynaGtaAt1561550.9935911282-11284
ORF1ab/nsp6104S104NS3673NnonsynaGTaAC15610.0064102611282-11284
ORF1ab/nsp6104S104del1S3673del1delagTag-1221180.96721311282-11284
ORF1ab/nsp6104S104del1S3673del1delaGTa-N12230.024590211282-11284
ORF1ab/nsp6104S104del1S3673del1delAgt-gt12210.0081967211282-11284
ORF1ab/nsp6104S104GS3673GnonsynAgtGgt81790.97530911282-11284
ORF1ab/nsp6104S104GS3673GnonsynAgTGgA8120.024691411282-11284
ORF1ab/nsp6104S104RS3673RnonsynagTagG65560.86153811282-11284
ORF1ab/nsp6104S104RS3673RnonsynagTagA6580.12307711282-11284
ORF1ab/nsp6104S104RS3673RnonsynAgtCgt6510.015384611282-11284
ORF1ab/nsp6104S104SS3673SsynagTagC4747111282-11284
ORF1ab/nsp6104S104MS3673MnonsynaGTaTG4545111282-11284
ORF1ab/nsp6104S104TS3673TnonsynaGtaCt3333111282-11284
ORF1ab/nsp6104S104IS3673InonsynaGtaTt2323111282-11284
ORF1ab/nsp6104S104del2S3673del2delaGTa--15110.73333311282-11284
ORF1ab/nsp6104S104del2S3673del2delAGt--t1520.13333311282-11284
ORF1ab/nsp6104S104del2S3673del2delAGT--N1520.13333311282-11284
ORF1ab/nsp6104S104CS3673CnonsynAgtTgt99111282-11284
ORF1ab/nsp6104S104KS3673KnonsynaGTaAA55111282-11284
ORF1ab/nsp6104S104VS3673VnonsynAGtGTt22111282-11284
ORF1ab/nsp6104S104XS3673XnonsynAgTTgA210.511282-11284
ORF1ab/nsp6104S104XS3673XnonsynAGTTAA210.511282-11284
ORF1ab/nsp6104S104YS3673YnonsynAGtTAt11111282-11284
ORF1ab/nsp6104S104FS3673FnonsynAGtTTt11111282-11284
ORF1ab/nsp6104S104AS3673AnonsynAGtGCt11111282-11284

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/nsp6104S104delAGT---13881388All0.000265
ORF1ab/nsp6104S104delAGT---460460B.1.6270.929293
ORF1ab/nsp6104S104delAGT---282282B.1.6310.949495
ORF1ab/nsp6104S104delAGT---257257B.1.617.20.000968
ORF1ab/nsp6104S104NaGtaAt155156All0.00003
ORF1ab/nsp6104S104NaGTaAC1156All0
ORF1ab/nsp6104S104del1agTag-118122All0.000023
ORF1ab/nsp6104S104del1aGTa-N3122All0.000001
ORF1ab/nsp6104S104del1Agt-gt1122All0
ORF1ab/nsp6104S104del1agTag-9191C.370.010562
ORF1ab/nsp6104S104GAgtGgt7981All0.000015
ORF1ab/nsp6104S104GAgTGgA281All0
ORF1ab/nsp6104S104RagTagG5665All0.000011
ORF1ab/nsp6104S104RagTagA865All0.000002
ORF1ab/nsp6104S104RAgtCgt165All0
ORF1ab/nsp6104S104delAGT---4848AY.1020.001273
ORF1ab/nsp6104S104SagTagC4747All0.000009
ORF1ab/nsp6104S104MaGTaTG4545All0.000009
ORF1ab/nsp6104S104RagTagG4444AY.40.000068
ORF1ab/nsp6104S104delAGT---3737B.1.5750.011226
ORF1ab/nsp6104S104MaGTaTG3636B.1.1.70.000032
ORF1ab/nsp6104S104delAGT---3434AY.440.000207
ORF1ab/nsp6104S104TaGtaCt3333All0.000006
ORF1ab/nsp6104S104NaGtaAt3030B.1.20.000264
ORF1ab/nsp6104S104GAgtGgt2929B.1.1.70.000026
ORF1ab/nsp6104S104NaGtaAt2727AY.250.000162
ORF1ab/nsp6104S104delAGT---2626B.1.1.70.000023
ORF1ab/nsp6104S104IaGtaTt2323All0.000004
ORF1ab/nsp6104S104delAGT---2222AY.390.000544
ORF1ab/nsp6104S104delAGT---2222B.1.10.000399
ORF1ab/nsp6104S104delAGT---2121AY.250.000126
ORF1ab/nsp6104S104delAGT---2020AY.1030.000124
ORF1ab/nsp6104S104NaGtaAt1920AY.440.000116
ORF1ab/nsp6104S104NaGTaAC120AY.440.000006
ORF1ab/nsp6104S104delAGT---1818AY.40.000028
ORF1ab/nsp6104S104NaGtaAt1616B.1.4290.000376
ORF1ab/nsp6104S104del2aGTa--1115All0.000002
ORF1ab/nsp6104S104del2AGt--t215All0
ORF1ab/nsp6104S104del2AGT--N215All0
ORF1ab/nsp6104S104delAGT---1515AY.1200.000558
ORF1ab/nsp6104S104SagTagC1515B.1.1.70.000013
ORF1ab/nsp6104S104TaGtaCt1515B.1.617.20.000056
ORF1ab/nsp6104S104delAGT---1414B.10.000128
ORF1ab/nsp6104S104TaGtaCt1313AY.1190.000459
ORF1ab/nsp6104S104delAGT---1212B.1.1.2320.021779
ORF1ab/nsp6104S104CAgtTgt99All0.000002
ORF1ab/nsp6104S104delAGT---99AY.430.00004
ORF1ab/nsp6104S104del2aGTa--79B.1.1.70.000006
ORF1ab/nsp6104S104RagTagG59B.1.1.70.000004
ORF1ab/nsp6104S104RagTagA49B.1.1.70.000004
ORF1ab/nsp6104S104del2AGT--N29B.1.1.70.000002
ORF1ab/nsp6104S104delAGT---99P.10.000142
ORF1ab/nsp6104S104GAgtGgt88B.1.6280.002819
ORF1ab/nsp6104S104GAgtGgt88P.1.10.002541
ORF1ab/nsp6104S104del1agTag-77B.1.1.70.000006
ORF1ab/nsp6104S104NaGtaAt77B.1.1.70.000006
ORF1ab/nsp6104S104delAGT---66B.1.1.5190.000238
ORF1ab/nsp6104S104GAgtGgt66B.1.5250.000679
ORF1ab/nsp6104S104del1agTag-66P.10.000095
ORF1ab/nsp6104S104NaGtaAt66P.10.000095
ORF1ab/nsp6104S104KaGTaAA55All0.000001
ORF1ab/nsp6104S104delAGT---55AY.3.10.000426
ORF1ab/nsp6104S104SagTagC55AY.390.000124
ORF1ab/nsp6104S104NaGtaAt55B.1.10.000091
ORF1ab/nsp6104S104delAGT---55B.1.20.000044
ORF1ab/nsp6104S104MaGTaTG55P.10.000079
ORF1ab/nsp6104S104RagTagA440.222222
ORF1ab/nsp6104S104GAgTGgA240.111111
ORF1ab/nsp6104S104GAgtGgt240.111111
ORF1ab/nsp6104S104delAGT---44AY.20.001425
ORF1ab/nsp6104S104delAGT---44AY.30.00004
ORF1ab/nsp6104S104NaGtaAt44AY.40.000006
ORF1ab/nsp6104S104SagTagC44AY.40.000006
ORF1ab/nsp6104S104delAGT---44AY.50.000083
ORF1ab/nsp6104S104NaGtaAt44B.1.1.370.000771
ORF1ab/nsp6104S104KaGTaAA44B.1.1.70.000004
ORF1ab/nsp6104S104IaGtaTt44B.1.1.70.000004
ORF1ab/nsp6104S104RagTagG44B.1.5260.000094
ORF1ab/nsp6104S104NaGtaAt44B.1.617.20.000015
ORF1ab/nsp6104S104SagTagC44B.1.617.20.000015
ORF1ab/nsp6104S104NaGtaAt33AY.290.000047
ORF1ab/nsp6104S104del1agTag-33B.10.000027
ORF1ab/nsp6104S104IaGtaTt33B.10.000027
ORF1ab/nsp6104S104NaGtaAt33B.1.1.330.001263
ORF1ab/nsp6104S104delAGT---33B.1.177.40.000633
ORF1ab/nsp6104S104delAGT---33B.1.5650.002431
ORF1ab/nsp6104S104del1aGTa-N33B.1.6310.010101
ORF1ab/nsp6104S104GAgtGgt33P.1.170.000485
ORF1ab/nsp6104S104del1agTag-33P.1.70.000958
ORF1ab/nsp6104S104SagTagC220.111111
ORF1ab/nsp6104S104VAGtGTt22All0
ORF1ab/nsp6104S104XAGTTAA12All0
ORF1ab/nsp6104S104XAgTTgA12All0
ORF1ab/nsp6104S104NaGtaAt22AY.1020.000053
ORF1ab/nsp6104S104delAGT---22AY.1170.000169
ORF1ab/nsp6104S104GAgtGgt22AY.390.000049
ORF1ab/nsp6104S104NaGtaAt22AY.4.50.000215
ORF1ab/nsp6104S104NaGtaAt22AY.420.00008
ORF1ab/nsp6104S104NaGtaAt22AY.430.000009
ORF1ab/nsp6104S104CAgtTgt22AY.430.000009
ORF1ab/nsp6104S104del1agTag-22AY.430.000009
ORF1ab/nsp6104S104SagTagC22B.10.000018
ORF1ab/nsp6104S104NaGtaAt22B.10.000018
ORF1ab/nsp6104S104delAGT---22B.1.1.10.000653
ORF1ab/nsp6104S104delAGT---22B.1.1.2190.01
ORF1ab/nsp6104S104IaGtaTt22B.1.1.3020.004149
ORF1ab/nsp6104S104CAgtTgt22B.1.1.70.000002
ORF1ab/nsp6104S104XAGTTAA12B.1.1.70.000001
ORF1ab/nsp6104S104XAgTTgA12B.1.1.70.000001
ORF1ab/nsp6104S104NaGtaAt22B.1.1600.000062
ORF1ab/nsp6104S104delAGT---22B.1.177.730.001133
ORF1ab/nsp6104S104SagTagC22B.1.20.000018
ORF1ab/nsp6104S104del2aGTa--22B.1.214.40.018182
ORF1ab/nsp6104S104delAGT---22B.1.3510.000059
ORF1ab/nsp6104S104delAGT---22B.1.36.80.002
ORF1ab/nsp6104S104NaGtaAt22B.1.6210.000177
ORF1ab/nsp6104S104del1agTag-22B.1.6280.000705
ORF1ab/nsp6104S104GAgtGgt22C.370.000232
ORF1ab/nsp6104S104GAgtGgt22P.10.000032
ORF1ab/nsp6104S104SagTagC22P.10.000032
ORF1ab/nsp6104S104MaGTaTG22P.1.140.000096
ORF1ab/nsp6104S104GAgtGgt22P.1.150.000465
ORF1ab/nsp6104S104GAgtGgt22P.1.20.002312
ORF1ab/nsp6104S104delAGT---22P.1.70.000639
ORF1ab/nsp6104S104IaGtaTt110.055556
ORF1ab/nsp6104S104delAGT---11A.2.50.000499
ORF1ab/nsp6104S104YAGtTAt11All0
ORF1ab/nsp6104S104FAGtTTt11All0
ORF1ab/nsp6104S104AAGtGCt11All0
ORF1ab/nsp6104S104delAGT---11AY.1000.000046
ORF1ab/nsp6104S104IaGtaTt11AY.1020.000027
ORF1ab/nsp6104S104GAgtGgt11AY.1020.000027
ORF1ab/nsp6104S104CAgtTgt11AY.1030.000006
ORF1ab/nsp6104S104IaGtaTt11AY.1030.000006
ORF1ab/nsp6104S104SagTagC11AY.1030.000006
ORF1ab/nsp6104S104delAGT---11AY.1040.001984
ORF1ab/nsp6104S104delAGT---11AY.1060.000335
ORF1ab/nsp6104S104GAgtGgt11AY.1100.000113
ORF1ab/nsp6104S104delAGT---11AY.1190.000035
ORF1ab/nsp6104S104NaGtaAt11AY.1200.000037
ORF1ab/nsp6104S104SagTagC11AY.1200.000037
ORF1ab/nsp6104S104IaGtaTt11AY.1200.000037
ORF1ab/nsp6104S104delAGT---11AY.120.20.001285
ORF1ab/nsp6104S104delAGT---11AY.200.000039
ORF1ab/nsp6104S104delAGT---11AY.230.00007
ORF1ab/nsp6104S104NaGtaAt11AY.260.000028
ORF1ab/nsp6104S104SagTagC11AY.260.000028
ORF1ab/nsp6104S104delAGT---11AY.290.000016
ORF1ab/nsp6104S104IaGtaTt11AY.30.00001
ORF1ab/nsp6104S104RagTagG11AY.340.000097
ORF1ab/nsp6104S104IaGtaTt11AY.390.000025
ORF1ab/nsp6104S104GAgtGgt11AY.40.000002
ORF1ab/nsp6104S104delAGT---11AY.4.2.10.000149
ORF1ab/nsp6104S104VAGtGTt11AY.430.000004
ORF1ab/nsp6104S104RagTagG11AY.430.000004
ORF1ab/nsp6104S104GAgtGgt11AY.430.000004
ORF1ab/nsp6104S104IaGtaTt11AY.430.000004
ORF1ab/nsp6104S104del1Agt-gt11AY.440.000006
ORF1ab/nsp6104S104SagTagC11AY.440.000006
ORF1ab/nsp6104S104delAGT---11AY.450.000122
ORF1ab/nsp6104S104delAGT---11AY.46.60.000072
ORF1ab/nsp6104S104RAgtCgt11AY.470.000031
ORF1ab/nsp6104S104SagTagC11AY.50.000021
ORF1ab/nsp6104S104CAgtTgt11AY.60.000041
ORF1ab/nsp6104S104delAGT---11AY.610.000105
ORF1ab/nsp6104S104delAGT---11AY.740.000116
ORF1ab/nsp6104S104delAGT---11AY.750.000056
ORF1ab/nsp6104S104delAGT---11AY.75.10.00018
ORF1ab/nsp6104S104delAGT---11AY.780.001541
ORF1ab/nsp6104S104delAGT---11AY.980.000079
ORF1ab/nsp6104S104delAGT---11AY.99.20.000092
ORF1ab/nsp6104S104NaGtaAt11B0.000128
ORF1ab/nsp6104S104KaGTaAA11B0.000128
ORF1ab/nsp6104S104delAGT---11B0.000128
ORF1ab/nsp6104S104AAGtGCt11B.10.000009
ORF1ab/nsp6104S104GAgtGgt11B.10.000009
ORF1ab/nsp6104S104CAgtTgt11B.10.000009
ORF1ab/nsp6104S104del2aGTa--11B.1.10.000018
ORF1ab/nsp6104S104delAGT---11B.1.1.1530.001095
ORF1ab/nsp6104S104IaGtaTt11B.1.1.1760.000439
ORF1ab/nsp6104S104NaGtaAt11B.1.1.2770.000759
ORF1ab/nsp6104S104delAGT---11B.1.1.3010.001179
ORF1ab/nsp6104S104SagTagC11B.1.1.4340.000349
ORF1ab/nsp6104S104TaGtaCt11B.1.1.5190.00004
ORF1ab/nsp6104S104delAGT---11B.1.1.5250.005464
ORF1ab/nsp6104S104FAGtTTt11B.1.1.70.000001
ORF1ab/nsp6104S104TaGtaCt11B.1.1.70.000001
ORF1ab/nsp6104S104YAGtTAt11B.1.1.70.000001
ORF1ab/nsp6104S104SagTagC11B.1.1.700.000341
ORF1ab/nsp6104S104NaGtaAt11B.1.110.30.000718
ORF1ab/nsp6104S104delAGT---11B.1.1600.000031
ORF1ab/nsp6104S104delAGT---11B.1.1770.000013
ORF1ab/nsp6104S104GAgtGgt11B.1.1770.000013
ORF1ab/nsp6104S104SagTagC11B.1.1770.000013
ORF1ab/nsp6104S104CAgtTgt11B.1.1770.000013
ORF1ab/nsp6104S104TaGtaCt11B.1.177.40.000211
ORF1ab/nsp6104S104NaGtaAt11B.1.177.430.001477
ORF1ab/nsp6104S104IaGtaTt11B.1.177.600.000218
ORF1ab/nsp6104S104NaGtaAt11B.1.177.600.000218
ORF1ab/nsp6104S104del2AGt--t11B.1.20.000009
ORF1ab/nsp6104S104MaGTaTG11B.1.20.000009
ORF1ab/nsp6104S104del1agTag-11B.1.20.000009
ORF1ab/nsp6104S104delAGT---11B.1.2210.000071
ORF1ab/nsp6104S104NaGtaAt11B.1.2210.000071
ORF1ab/nsp6104S104delAGT---11B.1.2340.000132
ORF1ab/nsp6104S104GAgtGgt11B.1.2400.000216
ORF1ab/nsp6104S104IaGtaTt11B.1.2410.000812
ORF1ab/nsp6104S104delAGT---11B.1.2580.000067
ORF1ab/nsp6104S104NaGtaAt11B.1.258.140.00098
ORF1ab/nsp6104S104IaGtaTt11B.1.3510.00003
ORF1ab/nsp6104S104GAgtGgt11B.1.3510.00003
ORF1ab/nsp6104S104delAGT---11B.1.351.30.000876
ORF1ab/nsp6104S104GAgtGgt11B.1.351.50.0006
ORF1ab/nsp6104S104CAgtTgt11B.1.4270.00005
ORF1ab/nsp6104S104delAGT---11B.1.4270.00005
ORF1ab/nsp6104S104NaGtaAt11B.1.4270.00005
ORF1ab/nsp6104S104TaGtaCt11B.1.4290.000024
ORF1ab/nsp6104S104GAgtGgt11B.1.4290.000024
ORF1ab/nsp6104S104IaGtaTt11B.1.4290.000024
ORF1ab/nsp6104S104NaGtaAt11B.1.4700.001404
ORF1ab/nsp6104S104NaGtaAt11B.1.5170.000427
ORF1ab/nsp6104S104VAGtGTt11B.1.5260.000024
ORF1ab/nsp6104S104IaGtaTt11B.1.5260.000024
ORF1ab/nsp6104S104GAgtGgt11B.1.5260.000024
ORF1ab/nsp6104S104SagTagC11B.1.5300.007143
ORF1ab/nsp6104S104IaGtaTt11B.1.5640.000426
ORF1ab/nsp6104S104del1agTag-11B.1.5800.004065
ORF1ab/nsp6104S104GAgtGgt11B.1.5950.000261
ORF1ab/nsp6104S104RagTagG11B.1.621.10.000506
ORF1ab/nsp6104S104GAgtGgt11B.1.6250.002353
ORF1ab/nsp6104S104MaGTaTG11B.1.6280.000352
ORF1ab/nsp6104S104delAGT---11B.1.6280.000352
ORF1ab/nsp6104S104delAGT---11B.1.6300.005236
ORF1ab/nsp6104S104del2aGTa--11B.1.6310.003367
ORF1ab/nsp6104S104SagTagC11B.1.6370.000073
ORF1ab/nsp6104S104delAGT---11C.1.20.004255
ORF1ab/nsp6104S104del2AGt--t11C.370.000116
ORF1ab/nsp6104S104TaGtaCt11D.20.000075
ORF1ab/nsp6104S104del1agTag-11D.20.000075
ORF1ab/nsp6104S104SagTagC11D.20.000075
ORF1ab/nsp6104S104delAGT---11N.40.004255
ORF1ab/nsp6104S104NaGtaAt11P.1.140.000048
ORF1ab/nsp6104S104del1agTag-11P.1.150.000232

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.