CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp13 : CodonNum = 390

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/nsp13390R390RR5714RsynagAagG619661430.99144617404-17406
ORF1ab/nsp13390R390RR5714RsynAgaCga6196490.0079083317404-17406
ORF1ab/nsp13390R390RR5714RsynAgACgG619630.00048418317404-17406
ORF1ab/nsp13390R390RR5714RsynAgACgT619610.00016139417404-17406
ORF1ab/nsp13390R390KR5714KnonsynaGaaAa35320.91428617404-17406
ORF1ab/nsp13390R390KR5714KnonsynaGAaAG3530.085714317404-17406
ORF1ab/nsp13390R390IR5714InonsynaGaaTa1212117404-17406
ORF1ab/nsp13390R390XR5714XnonsynAgaTga960.66666717404-17406
ORF1ab/nsp13390R390XR5714XnonsynAGaTAa930.33333317404-17406
ORF1ab/nsp13390R390QR5714QnonsynAGaCAa740.57142917404-17406
ORF1ab/nsp13390R390QR5714QnonsynAGACAG730.42857117404-17406
ORF1ab/nsp13390R390SR5714SnonsynagAagT55117404-17406
ORF1ab/nsp13390R390NR5714NnonsynaGAaAT33117404-17406
ORF1ab/nsp13390R390delR5714deldelAGA---33117404-17406
ORF1ab/nsp13390R390TR5714TnonsynaGaaCa22117404-17406
ORF1ab/nsp13390R390CR5714CnonsynAgATgT22117404-17406
ORF1ab/nsp13390R390YR5714YnonsynAGATAT22117404-17406
ORF1ab/nsp13390R390GR5714GnonsynAgaGga22117404-17406
ORF1ab/nsp13390R390LR5714LnonsynAGaTTa11117404-17406
ORF1ab/nsp13390R390ER5714EnonsynAGaGAa11117404-17406
ORF1ab/nsp13390R390HR5714HnonsynAGACAT11117404-17406

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/nsp13390R390RagAagG61436196All0.001175
ORF1ab/nsp13390R390RAgaCga496196All0.000009
ORF1ab/nsp13390R390RAgACgG36196All0.000001
ORF1ab/nsp13390R390RAgACgT16196All0
ORF1ab/nsp13390R390RagAagG54055405AY.130.87009
ORF1ab/nsp13390R390RagAagG7389B.1.1.70.000065
ORF1ab/nsp13390R390RAgaCga1689B.1.1.70.000014
ORF1ab/nsp13390R390RagAagG7272AY.40.000112
ORF1ab/nsp13390R390RagAagG7070AY.750.003922
ORF1ab/nsp13390R390RagAagG5050AY.46.50.009921
ORF1ab/nsp13390R390RagAagG3944B.10.000357
ORF1ab/nsp13390R390RAgaCga544B.10.000046
ORF1ab/nsp13390R390RagAagG4040AY.510.036364
ORF1ab/nsp13390R390KaGaaAa3235All0.000006
ORF1ab/nsp13390R390KaGAaAG335All0.000001
ORF1ab/nsp13390R390RagAagG3434B.1.5260.000799
ORF1ab/nsp13390R390RagAagG2434B.1.617.20.00009
ORF1ab/nsp13390R390RAgaCga1034B.1.617.20.000038
ORF1ab/nsp13390R390RagAagG3131AY.50.00064
ORF1ab/nsp13390R390RagAagG2525AY.540.002384
ORF1ab/nsp13390R390RagAagG2323AY.620.010022
ORF1ab/nsp13390R390RagAagG1416B.1.10.000254
ORF1ab/nsp13390R390RAgaCga116B.1.10.000018
ORF1ab/nsp13390R390RAgACgG116B.1.10.000018
ORF1ab/nsp13390R390RagAagG1414AY.400.0135
ORF1ab/nsp13390R390RagAagG1313B.1.20.000114
ORF1ab/nsp13390R390IaGaaTa1212All0.000002
ORF1ab/nsp13390R390RagAagG1212AY.730.007984
ORF1ab/nsp13390R390RagAagG1111AY.250.000066
ORF1ab/nsp13390R390RagAagG1010AY.440.000061
ORF1ab/nsp13390R390XAgaTga69All0.000001
ORF1ab/nsp13390R390XAGaTAa39All0.000001
ORF1ab/nsp13390R390RagAagG99AY.390.000222
ORF1ab/nsp13390R390RagAagG99B.1.2580.000599
ORF1ab/nsp13390R390RagAagG78AY.4.20.000152
ORF1ab/nsp13390R390RAgaCga18AY.4.20.000022
ORF1ab/nsp13390R390KaGaaAa570.277778
ORF1ab/nsp13390R390KaGAaAG270.111111
ORF1ab/nsp13390R390QAGaCAa47All0.000001
ORF1ab/nsp13390R390QAGACAG37All0.000001
ORF1ab/nsp13390R390RagAagG77AY.1030.000043
ORF1ab/nsp13390R390RagAagG77AY.430.000031
ORF1ab/nsp13390R390RagAagG77B0.000895
ORF1ab/nsp13390R390XAgaTga360.166667
ORF1ab/nsp13390R390XAGaTAa360.166667
ORF1ab/nsp13390R390RagAagG260.111111
ORF1ab/nsp13390R390RAgACgG260.111111
ORF1ab/nsp13390R390RAgaCga260.111111
ORF1ab/nsp13390R390RagAagG66AY.1190.000212
ORF1ab/nsp13390R390RagAagG66AY.650.003198
ORF1ab/nsp13390R390RagAagG66AY.9.20.00022
ORF1ab/nsp13390R390KaGaaAa66B.1.20.000053
ORF1ab/nsp13390R390SagAagT55All0.000001
ORF1ab/nsp13390R390RagAagG35AY.200.000117
ORF1ab/nsp13390R390RAgaCga25AY.200.000078
ORF1ab/nsp13390R390RagAagG55AY.75.10.000902
ORF1ab/nsp13390R390RagAagG55AY.840.002187
ORF1ab/nsp13390R390RagAagG45B.1.1600.000125
ORF1ab/nsp13390R390RAgaCga15B.1.1600.000031
ORF1ab/nsp13390R390RagAagG55B.1.4270.000252
ORF1ab/nsp13390R390RagAagG55P.1.140.000239
ORF1ab/nsp13390R390QAGACAG240.111111
ORF1ab/nsp13390R390QAGaCAa240.111111
ORF1ab/nsp13390R390KaGaaAa44AY.1030.000025
ORF1ab/nsp13390R390RagAagG44AY.260.000113
ORF1ab/nsp13390R390RagAagG44AY.30.00004
ORF1ab/nsp13390R390RagAagG44AY.520.003257
ORF1ab/nsp13390R390RagAagG44AY.610.000419
ORF1ab/nsp13390R390KaGaaAa44B.1.1.2970.008949
ORF1ab/nsp13390R390RAgaCga24B.1.2210.000142
ORF1ab/nsp13390R390RAgACgT14B.1.2210.000071
ORF1ab/nsp13390R390RagAagG14B.1.2210.000071
ORF1ab/nsp13390R390RagAagG44B.1.3510.000119
ORF1ab/nsp13390R390RagAagG44B.1.438.10.000429
ORF1ab/nsp13390R390delAGA---33All0.000001
ORF1ab/nsp13390R390NaGAaAT33All0.000001
ORF1ab/nsp13390R390RAgaCga33AY.1000.000138
ORF1ab/nsp13390R390RAgaCga33AY.1020.00008
ORF1ab/nsp13390R390KaGaaAa33AY.250.000018
ORF1ab/nsp13390R390RagAagG33AY.340.000291
ORF1ab/nsp13390R390IaGaaTa33B.10.000027
ORF1ab/nsp13390R390KaGaaAa23B.1.10.000036
ORF1ab/nsp13390R390KaGAaAG13B.1.10.000018
ORF1ab/nsp13390R390RagAagG33B.1.1770.00004
ORF1ab/nsp13390R390RagAagG33B.1.4130.012766
ORF1ab/nsp13390R390RagAagG33P.10.000047
ORF1ab/nsp13390R390SagAagT220.111111
ORF1ab/nsp13390R390NaGAaAT220.111111
ORF1ab/nsp13390R390CAgATgT220.111111
ORF1ab/nsp13390R390YAGATAT220.111111
ORF1ab/nsp13390R390YAGATAT22All0
ORF1ab/nsp13390R390GAgaGga22All0
ORF1ab/nsp13390R390TaGaaCa22All0
ORF1ab/nsp13390R390CAgATgT22All0
ORF1ab/nsp13390R390RagAagG22AY.1170.000169
ORF1ab/nsp13390R390KaGaaAa22AY.40.000003
ORF1ab/nsp13390R390RagAagG22AY.590.001059
ORF1ab/nsp13390R390RagAagG22AY.850.000854
ORF1ab/nsp13390R390RagAagG22AY.90.000135
ORF1ab/nsp13390R390RagAagG22AY.98.10.000097
ORF1ab/nsp13390R390RagAagG22AY.99.20.000184
ORF1ab/nsp13390R390QAGaCAa12B.1.10.000018
ORF1ab/nsp13390R390QAGACAG12B.1.10.000018
ORF1ab/nsp13390R390RagAagG22B.1.1.280.000622
ORF1ab/nsp13390R390delAGA---22B.1.1.70.000002
ORF1ab/nsp13390R390RagAagG22B.1.1.700.000682
ORF1ab/nsp13390R390IaGaaTa22B.1.20.000018
ORF1ab/nsp13390R390KaGaaAa22B.1.2210.000142
ORF1ab/nsp13390R390RagAagG22B.1.4290.000047
ORF1ab/nsp13390R390RagAagG22B.1.5580.009132
ORF1ab/nsp13390R390RagAagG22B.1.5960.000174
ORF1ab/nsp13390R390IaGaaTa11A0.000387
ORF1ab/nsp13390R390RagAagG11AE.80.000489
ORF1ab/nsp13390R390HAGACAT11All0
ORF1ab/nsp13390R390LAGaTTa11All0
ORF1ab/nsp13390R390EAGaGAa11All0
ORF1ab/nsp13390R390KaGaaAa11AY.1020.000027
ORF1ab/nsp13390R390RagAagG11AY.1060.000335
ORF1ab/nsp13390R390RagAagG11AY.1100.000113
ORF1ab/nsp13390R390RagAagG11AY.1160.000287
ORF1ab/nsp13390R390RagAagG11AY.16.10.00047
ORF1ab/nsp13390R390RagAagG11AY.230.00007
ORF1ab/nsp13390R390RagAagG11AY.29.10.000221
ORF1ab/nsp13390R390RagAagG11AY.3.10.000085
ORF1ab/nsp13390R390RagAagG11AY.330.000067
ORF1ab/nsp13390R390EAGaGAa11AY.440.000006
ORF1ab/nsp13390R390RagAagG11AY.450.000122
ORF1ab/nsp13390R390RagAagG11AY.46.40.000165
ORF1ab/nsp13390R390RagAagG11AY.5.40.000277
ORF1ab/nsp13390R390RagAagG11AY.670.000464
ORF1ab/nsp13390R390RagAagG11AY.720.001361
ORF1ab/nsp13390R390RagAagG11AY.900.000684
ORF1ab/nsp13390R390RagAagG11AY.930.000273
ORF1ab/nsp13390R390GAgaGga11B.10.000009
ORF1ab/nsp13390R390XAgaTga11B.10.000009
ORF1ab/nsp13390R390RagAagG11B.1.1.1530.001095
ORF1ab/nsp13390R390IaGaaTa11B.1.1.1640.005155
ORF1ab/nsp13390R390XAgaTga11B.1.1.1640.005155
ORF1ab/nsp13390R390RagAagG11B.1.1.2140.000055
ORF1ab/nsp13390R390RagAagG11B.1.1.2160.00089
ORF1ab/nsp13390R390SagAagT11B.1.1.2220.000204
ORF1ab/nsp13390R390RagAagG11B.1.1.2270.004348
ORF1ab/nsp13390R390RagAagG11B.1.1.2910.000742
ORF1ab/nsp13390R390RagAagG11B.1.1.3060.000438
ORF1ab/nsp13390R390RagAagG11B.1.1.3160.000925
ORF1ab/nsp13390R390XAgaTga11B.1.1.3420.0625
ORF1ab/nsp13390R390LAGaTTa11B.1.1.3420.0625
ORF1ab/nsp13390R390IaGaaTa11B.1.1.3420.0625
ORF1ab/nsp13390R390RagAagG11B.1.1.370.000193
ORF1ab/nsp13390R390RagAagG11B.1.1.4090.002833
ORF1ab/nsp13390R390GAgaGga11B.1.1.70.000001
ORF1ab/nsp13390R390IaGaaTa11B.1.1570.002985
ORF1ab/nsp13390R390KaGaaAa11B.1.1600.000031
ORF1ab/nsp13390R390SagAagT11B.1.2210.000071
ORF1ab/nsp13390R390QAGaCAa11B.1.2210.000071
ORF1ab/nsp13390R390NaGAaAT11B.1.2210.000071
ORF1ab/nsp13390R390HAGACAT11B.1.2210.000071
ORF1ab/nsp13390R390TaGaaCa11B.1.2430.00007
ORF1ab/nsp13390R390RagAagG11B.1.2980.002114
ORF1ab/nsp13390R390RagAagG11B.1.351.50.0006
ORF1ab/nsp13390R390RagAagG11B.1.36.100.004785
ORF1ab/nsp13390R390IaGaaTa11B.1.4160.001269
ORF1ab/nsp13390R390IaGaaTa11B.1.4320.011236
ORF1ab/nsp13390R390delAGA---11B.1.4340.052632
ORF1ab/nsp13390R390RagAagG11B.1.466.20.000391
ORF1ab/nsp13390R390IaGaaTa11B.1.5640.000426
ORF1ab/nsp13390R390RAgaCga11B.1.5950.000261
ORF1ab/nsp13390R390KaGaaAa11B.1.5960.000087
ORF1ab/nsp13390R390KaGaaAa11B.1.617.20.000004
ORF1ab/nsp13390R390RagAagG11B.30.000831
ORF1ab/nsp13390R390RagAagG11C.10.002392
ORF1ab/nsp13390R390RAgaCga11C.370.000116
ORF1ab/nsp13390R390TaGaaCa11D.20.000075
ORF1ab/nsp13390R390SagAagT11D.20.000075
ORF1ab/nsp13390R390RAgaCga11Q.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.