CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 668

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
S668A668AsyngcAgcT7665820.75979123564-23566
S668A668AsyngcAgcG7661270.16579623564-23566
S668A668AsyngcAgcC766570.074412523564-23566
S668A668SnonsynGcaTca1971960.99492423564-23566
S668A668SnonsynGcATcC19710.0050761423564-23566
S668A668deldelGCA---108108123564-23566
S668A668VnonsyngCagTa6464123564-23566
S668A668GnonsyngCagGa41400.9756123564-23566
S668A668GnonsyngCAgGC4110.024390223564-23566
S668A668TnonsynGcaAca15130.86666723564-23566
S668A668TnonsynGcAAcG1510.066666723564-23566
S668A668TnonsynGcAAcT1510.066666723564-23566
S668A668EnonsyngCagAa66123564-23566
S668A668RnonsynGCaAGa55123564-23566
S668A668del1delGca-ca420.523564-23566
S668A668del1delgcAgc-410.2523564-23566
S668A668del1delGcA-cT410.2523564-23566
S668A668DnonsyngCAgAT11123564-23566
S668A668PnonsynGcaCca11123564-23566
S668A668QnonsynGCACAG11123564-23566
S668A668XnonsynGCaTGa11123564-23566
S668A668CnonsynGCATGC11123564-23566
S668A668LnonsynGCACTG11123564-23566

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

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
S668A668AgcAgcT582766All0.000111
S668A668AgcAgcG127766All0.000024
S668A668AgcAgcC57766All0.000011
S668A668AgcAgcT347347B.1.20.003055
S668A668SGcaTca196197All0.000037
S668A668SGcATcC1197All0
S668A668delGCA---108108All0.000021
S668A668VgCagTa6464All0.000012
S668A668AgcAgcT5959B.1.5631
S668A668SGcaTca5454B.1.177.860.009906
S668A668AgcAgcT4246AY.440.000256
S668A668AgcAgcG346AY.440.000018
S668A668AgcAgcC146AY.440.000006
S668A668GgCagGa4041All0.000008
S668A668GgCAgGC141All0
S668A668AgcAgcT1937B.10.000174
S668A668AgcAgcG937B.10.000082
S668A668AgcAgcC937B.10.000082
S668A668GgCagGa3131AY.1210.004195
S668A668AgcAgcT1531B.1.1.70.000013
S668A668AgcAgcG1031B.1.1.70.000009
S668A668AgcAgcC631B.1.1.70.000005
S668A668SGcaTca2626B.1.1.70.000023
S668A668AgcAgcG1024AY.40.000016
S668A668AgcAgcC924AY.40.000014
S668A668AgcAgcT524AY.40.000008
S668A668AgcAgcG2424B.1.36.180.010084
S668A668AgcAgcT1222B.1.617.20.000045
S668A668AgcAgcG522B.1.617.20.000019
S668A668AgcAgcC522B.1.617.20.000019
S668A668AgcAgcG1718AY.30.000169
S668A668AgcAgcT118AY.30.00001
S668A668delGCA---1818B.10.000165
S668A668SGcaTca1717B.1.6370.001242
S668A668TGcaAca1315All0.000002
S668A668TGcAAcT115All0
S668A668TGcAAcG115All0
S668A668VgCagTa1313AY.40.00002
S668A668AgcAgcT712AY.430.000031
S668A668AgcAgcG312AY.430.000013
S668A668AgcAgcC212AY.430.000009
S668A668SGcaTca1212B.10.00011
S668A668AgcAgcT1111AY.300.004353
S668A668AgcAgcT99B.1.1.700.00307
S668A668SGcaTca88B.1.1770.000105
S668A668AgcAgcC68B.1.1770.000079
S668A668AgcAgcT18B.1.1770.000013
S668A668AgcAgcG18B.1.1770.000013
S668A668VgCagTa88B.1.20.00007
S668A668delGCA---88B.1.20.00007
S668A668AgcAgcT88B.1.5130.111111
S668A668SGcaTca88B.1.617.20.00003
S668A668AgcAgcT88C.1.20.034043
S668A668SGcaTca77AY.40.000011
S668A668VgCagTa77B.10.000064
S668A668delGCA---77B.1.1.70.000006
S668A668EgCagAa66All0.000001
S668A668SGcaTca66AY.1020.000159
S668A668AgcAgcT56AY.1020.000133
S668A668AgcAgcG16AY.1020.000027
S668A668AgcAgcG56AY.50.000103
S668A668AgcAgcT16AY.50.000021
S668A668delGCA---66P.10.000095
S668A668RGCaAGa55All0.000001
S668A668SGcaTca55AY.1030.000031
S668A668AgcAgcT35AY.1030.000019
S668A668AgcAgcC15AY.1030.000006
S668A668AgcAgcG15AY.1030.000006
S668A668delGCA---55AY.430.000022
S668A668AgcAgcT55B.1.1.3750.059524
S668A668VgCagTa55B.1.1.5190.000199
S668A668VgCagTa55B.1.1.70.000004
S668A668AgcAgcG55B.1.5170.002135
S668A668AgcAgcT45B.1.5960.000349
S668A668AgcAgcG15B.1.5960.000087
S668A668VgCagTa55P.1.140.000239
S668A668TGcaAca440.222222
S668A668del1Gca-ca24All0
S668A668del1GcA-cT14All0
S668A668del1gcAgc-14All0
S668A668AgcAgcG44AY.1130.00057
S668A668SGcaTca34B.1.10.000054
S668A668SGcATcC14B.1.10.000018
S668A668AgcAgcC44B.1.1600.000125
S668A668delGCA---44B.1.1770.000053
S668A668SGcaTca44B.1.20.000035
S668A668SGcaTca44B.1.2400.000862
S668A668AgcAgcG44B.1.3510.000119
S668A668delGCA---44B.1.5960.000349
S668A668VgCagTa44B.1.617.20.000015
S668A668SGcaTca33AY.250.000018
S668A668delGCA---33AY.250.000018
S668A668SGcaTca33AY.4.20.000065
S668A668SGcaTca33AY.430.000013
S668A668AgcAgcG33AY.540.000286
S668A668AgcAgcC33AY.980.000237
S668A668AgcAgcC23B.1.10.000036
S668A668AgcAgcG13B.1.10.000018
S668A668TGcaAca23B.1.1.70.000002
S668A668TGcAAcT13B.1.1.70.000001
S668A668SGcaTca33B.1.2430.000209
S668A668GgCagGa33B.1.617.20.000011
S668A668delGCA---33B.1.617.20.000011
S668A668delGCA---33B.1.6210.000266
S668A668delGCA---33P.1.150.000697
S668A668RGCaAGa220.111111
S668A668delGCA---220.111111
S668A668AgcAgcT22AY.200.000078
S668A668GgCagGa22AY.230.000139
S668A668AgcAgcG12AY.250.000006
S668A668AgcAgcT12AY.250.000006
S668A668AgcAgcC22AY.290.000032
S668A668VgCagTa22AY.30.00002
S668A668AgcAgcG22AY.350.000466
S668A668SGcaTca22AY.440.000012
S668A668SGcaTca22AY.5.40.000553
S668A668GgCagGa22AY.750.000112
S668A668SGcaTca22AY.75.10.000361
S668A668RGCaAGa22B.10.000018
S668A668VgCagTa22B.1.10.000036
S668A668delGCA---22B.1.10.000036
S668A668GgCagGa12B.1.10.000018
S668A668GgCAgGC12B.1.10.000018
S668A668AgcAgcC22B.1.1.1610.007067
S668A668SGcaTca22B.1.1.2690.002706
S668A668VgCagTa22B.1.1.2770.001517
S668A668SGcaTca22B.1.1.3260.003521
S668A668del1Gca-ca22B.1.1.70.000002
S668A668delGCA---22B.1.1600.000062
S668A668AgcAgcT22B.1.258.170.000208
S668A668SGcaTca22B.1.3510.000059
S668A668AgcAgcT22B.1.4290.000047
S668A668VgCagTa22B.1.5260.000047
S668A668delGCA---22B.1.5640.000852
S668A668AgcAgcT22B.1.6210.000177
S668A668AgcAgcG22C.110.021277
S668A668AgcAgcT22C.36.3.10.005435
S668A668SGcaTca22P.10.000032
S668A668delGCA---11A.2.20.001689
S668A668XGCaTGa11All0
S668A668QGCACAG11All0
S668A668DgCAgAT11All0
S668A668PGcaCca11All0
S668A668CGCATGC11All0
S668A668LGCACTG11All0
S668A668AgcAgcT11AY.1000.000046
S668A668delGCA---11AY.1030.000006
S668A668AgcAgcG11AY.1060.000335
S668A668DgCAgAT11AY.1130.000142
S668A668GgCagGa11AY.1170.000085
S668A668AgcAgcG11AY.1180.000063
S668A668VgCagTa11AY.1180.000063
S668A668SGcaTca11AY.1190.000035
S668A668AgcAgcG11AY.230.00007
S668A668SGcaTca11AY.230.00007
S668A668QGCACAG11AY.30.00001
S668A668SGcaTca11AY.340.000097
S668A668AgcAgcG11AY.34.10.00051
S668A668AgcAgcT11AY.390.000025
S668A668delGCA---11AY.390.000025
S668A668EgCagAa11AY.40.000002
S668A668TGcaAca11AY.40.000002
S668A668AgcAgcG11AY.4.20.000022
S668A668AgcAgcG11AY.400.000964
S668A668TGcaAca11AY.430.000004
S668A668delGCA---11AY.440.000006
S668A668AgcAgcT11AY.450.000122
S668A668SGcaTca11AY.46.20.000635
S668A668SGcaTca11AY.50.000021
S668A668VgCagTa11AY.50.000021
S668A668AgcAgcG11AY.520.000814
S668A668delGCA---11AY.670.000464
S668A668SGcaTca11AY.680.000274
S668A668AgcAgcT11AY.750.000056
S668A668AgcAgcG11AY.75.10.00018
S668A668delGCA---11AY.840.000437
S668A668SGcaTca11AY.9.20.000037
S668A668delGCA---11AY.9.20.000037
S668A668TGcaAca11AY.900.000684
S668A668SGcaTca11AY.980.000079
S668A668delGCA---11AY.990.001049
S668A668EgCagAa11B0.000128
S668A668AgcAgcC11B0.000128
S668A668LGCACTG11B.10.000009
S668A668TGcaAca11B.10.000009
S668A668EgCagAa11B.10.000009
S668A668del1gcAgc-11B.10.000009
S668A668PGcaCca11B.1.10.000018
S668A668EgCagAa11B.1.10.000018
S668A668TGcaAca11B.1.10.000018
S668A668CGCATGC11B.1.10.000018
S668A668XGCaTGa11B.1.10.000018
S668A668delGCA---11B.1.1.1970.037037
S668A668VgCagTa11B.1.1.2140.000055
S668A668VgCagTa11B.1.1.2220.000204
S668A668delGCA---11B.1.1.2220.000204
S668A668VgCagTa11B.1.1.2580.003257
S668A668RGCaAGa11B.1.1.2650.003155
S668A668delGCA---11B.1.1.3720.000689
S668A668VgCagTa11B.1.1.390.00051
S668A668TGcaAca11B.1.1.390.00051
S668A668AgcAgcC11B.1.1.4450.037037
S668A668delGCA---11B.1.160.330.004425
S668A668AgcAgcG11B.1.1630.02439
S668A668VgCagTa11B.1.1770.000013
S668A668delGCA---11B.1.177.120.000152
S668A668SGcaTca11B.1.177.200.001517
S668A668delGCA---11B.1.177.210.000076
S668A668delGCA---11B.1.177.350.000691
S668A668AgcAgcG11B.1.177.70.000165
S668A668AgcAgcG11B.1.177.820.000477
S668A668SGcaTca11B.1.177.90.001332
S668A668AgcAgcC11B.1.220.001318
S668A668AgcAgcC11B.1.2210.000071
S668A668delGCA---11B.1.2210.000071
S668A668delGCA---11B.1.2340.000132
S668A668AgcAgcG11B.1.2400.000216
S668A668delGCA---11B.1.2400.000216
S668A668AgcAgcC11B.1.2580.000067
S668A668delGCA---11B.1.258.220.002667
S668A668delGCA---11B.1.3250.006897
S668A668AgcAgcG11B.1.36.170.000494
S668A668AgcAgcG11B.1.36.350.002604
S668A668AgcAgcT11B.1.3620.001541
S668A668delGCA---11B.1.3710.001122
S668A668delGCA---11B.1.3750.00082
S668A668delGCA---11B.1.390.003906
S668A668AgcAgcT11B.1.4270.00005
S668A668TGcaAca11B.1.4270.00005
S668A668SGcaTca11B.1.4270.00005
S668A668delGCA---11B.1.4290.000024
S668A668SGcaTca11B.1.4290.000024
S668A668VgCagTa11B.1.4330.003195
S668A668EgCagAa11B.1.4380.006536
S668A668delGCA---11B.1.4500.011364
S668A668AgcAgcT11B.1.466.20.000391
S668A668delGCA---11B.1.4970.000315
S668A668delGCA---11B.1.5170.000427
S668A668SGcaTca11B.1.5260.000024
S668A668SGcaTca11B.1.5680.001111
S668A668AgcAgcT11B.1.5750.000303
S668A668delGCA---11B.1.5800.004065
S668A668delGCA---11B.1.5950.000261
S668A668EgCagAa11B.1.5950.000261
S668A668del1GcA-cT11B.1.617.20.000004
S668A668TGcAAcG11B.1.617.20.000004
S668A668delGCA---11B.1.6200.000946
S668A668delGCA---11B.1.6270.00202
S668A668VgCagTa11B.1.6300.005236
S668A668delGCA---11B.1.6380.052632
S668A668delGCA---11C.36.30.000567
S668A668delGCA---11C.370.000116
S668A668AgcAgcG11D.20.000075
S668A668SGcaTca11D.20.000075
S668A668AgcAgcT11P.10.000016
S668A668delGCA---11P.1.10.000318
S668A668delGCA---11P.1.130.000898
S668A668SGcaTca11P.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.