CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 558

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/nsp12558A558AA4950AsyngcTgcC231120250.87624415112-15114
ORF1ab/nsp12558A558AA4950AsyngcTgcA23112620.11337115112-15114
ORF1ab/nsp12558A558AA4950AsyngcTgcG2311240.010385115112-15114
ORF1ab/nsp12558A558SA4950SnonsynGctTct82730.89024415112-15114
ORF1ab/nsp12558A558SA4950SnonsynGCtAGt8230.036585415112-15114
ORF1ab/nsp12558A558SA4950SnonsynGcTTcC8220.024390215112-15114
ORF1ab/nsp12558A558SA4950SnonsynGCTAGC8220.024390215112-15114
ORF1ab/nsp12558A558SA4950SnonsynGcTTcA8210.012195115112-15114
ORF1ab/nsp12558A558SA4950SnonsynGcTTcG8210.012195115112-15114
ORF1ab/nsp12558A558del1A4950del1delGct-ct81800.98765415112-15114
ORF1ab/nsp12558A558del1A4950del1delgCtg-t8110.012345715112-15114
ORF1ab/nsp12558A558delA4950deldelGCT---3535115112-15114
ORF1ab/nsp12558A558VA4950VnonsyngCtgTt25240.9615112-15114
ORF1ab/nsp12558A558VA4950VnonsyngCTgTC2510.0415112-15114
ORF1ab/nsp12558A558TA4950TnonsynGctAct1070.715112-15114
ORF1ab/nsp12558A558TA4950TnonsynGcTAcC1020.215112-15114
ORF1ab/nsp12558A558TA4950TnonsynGcTAcA1010.115112-15114
ORF1ab/nsp12558A558GA4950GnonsyngCtgGt850.62515112-15114
ORF1ab/nsp12558A558GA4950GnonsyngCTgGC830.37515112-15114
ORF1ab/nsp12558A558FA4950FnonsynGCtTTt44115112-15114
ORF1ab/nsp12558A558PA4950PnonsynGctCct44115112-15114
ORF1ab/nsp12558A558CA4950CnonsynGCtTGt420.515112-15114
ORF1ab/nsp12558A558CA4950CnonsynGCTTGC420.515112-15114
ORF1ab/nsp12558A558DA4950DnonsyngCtgAt33115112-15114
ORF1ab/nsp12558A558IA4950InonsynGCtATt11115112-15114
ORF1ab/nsp12558A558YA4950YnonsynGCtTAt11115112-15114
ORF1ab/nsp12558A558HA4950HnonsynGCtCAt11115112-15114

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/nsp12558A558AgcTgcC20252311All0.000387
ORF1ab/nsp12558A558AgcTgcA2622311All0.00005
ORF1ab/nsp12558A558AgcTgcG242311All0.000005
ORF1ab/nsp12558A558AgcTgcC10361036AY.30.010304
ORF1ab/nsp12558A558AgcTgcC697697B.1.1.4330.992877
ORF1ab/nsp12558A558AgcTgcA180194B.1.1.70.000161
ORF1ab/nsp12558A558AgcTgcC9194B.1.1.70.000008
ORF1ab/nsp12558A558AgcTgcG5194B.1.1.70.000004
ORF1ab/nsp12558A558SGctTct7382All0.000014
ORF1ab/nsp12558A558SGCtAGt382All0.000001
ORF1ab/nsp12558A558SGcTTcC282All0
ORF1ab/nsp12558A558SGCTAGC282All0
ORF1ab/nsp12558A558SGcTTcG182All0
ORF1ab/nsp12558A558SGcTTcA182All0
ORF1ab/nsp12558A558del1Gct-ct8081All0.000015
ORF1ab/nsp12558A558del1gCtg-t181All0
ORF1ab/nsp12558A558AgcTgcC6166AY.40.000095
ORF1ab/nsp12558A558AgcTgcG366AY.40.000005
ORF1ab/nsp12558A558AgcTgcA266AY.40.000003
ORF1ab/nsp12558A558del1Gct-ct6666B.1.1.70.000059
ORF1ab/nsp12558A558AgcTgcA5252AZ.10.0451
ORF1ab/nsp12558A558delGCT---3535All0.000007
ORF1ab/nsp12558A558AgcTgcC2828AY.430.000124
ORF1ab/nsp12558A558AgcTgcC2628B.1.617.20.000098
ORF1ab/nsp12558A558AgcTgcA228B.1.617.20.000008
ORF1ab/nsp12558A558VgCtgTt2425All0.000005
ORF1ab/nsp12558A558VgCTgTC125All0
ORF1ab/nsp12558A558AgcTgcC1920B.1.10.000345
ORF1ab/nsp12558A558AgcTgcA120B.1.10.000018
ORF1ab/nsp12558A558AgcTgcC1717B.1.2580.001131
ORF1ab/nsp12558A558AgcTgcG1315B.1.1770.000171
ORF1ab/nsp12558A558AgcTgcC215B.1.1770.000026
ORF1ab/nsp12558A558AgcTgcC1315B.1.20.000114
ORF1ab/nsp12558A558AgcTgcA215B.1.20.000018
ORF1ab/nsp12558A558AgcTgcC1212AY.1170.001014
ORF1ab/nsp12558A558TGctAct710All0.000001
ORF1ab/nsp12558A558TGcTAcC210All0
ORF1ab/nsp12558A558TGcTAcA110All0
ORF1ab/nsp12558A558SGctTct1010AY.40.000016
ORF1ab/nsp12558A558AgcTgcC1010AY.440.000061
ORF1ab/nsp12558A558delGCT---1010B.1.1.70.000009
ORF1ab/nsp12558A558SGCtAGt390.166667
ORF1ab/nsp12558A558SGCTAGC290.111111
ORF1ab/nsp12558A558SGctTct290.111111
ORF1ab/nsp12558A558SGcTTcC290.111111
ORF1ab/nsp12558A558AgcTgcC99AY.250.000054
ORF1ab/nsp12558A558AgcTgcC99B.1.2340.001187
ORF1ab/nsp12558A558AgcTgcA89B.1.5250.000905
ORF1ab/nsp12558A558AgcTgcG19B.1.5250.000113
ORF1ab/nsp12558A558GgCtgGt58All0.000001
ORF1ab/nsp12558A558GgCTgGC38All0.000001
ORF1ab/nsp12558A558AgcTgcC68B.10.000055
ORF1ab/nsp12558A558AgcTgcA28B.10.000018
ORF1ab/nsp12558A558SGctTct77B.1.1.70.000006
ORF1ab/nsp12558A558AgcTgcC56AY.390.000124
ORF1ab/nsp12558A558AgcTgcG16AY.390.000025
ORF1ab/nsp12558A558SGctTct66AY.430.000027
ORF1ab/nsp12558A558VgCtgTt66D.20.00045
ORF1ab/nsp12558A558GgCtgGt350.166667
ORF1ab/nsp12558A558TGctAct350.166667
ORF1ab/nsp12558A558GgCTgGC250.111111
ORF1ab/nsp12558A558TGcTAcC250.111111
ORF1ab/nsp12558A558delGCT---55AY.250.00003
ORF1ab/nsp12558A558AgcTgcC55P.1.140.000239
ORF1ab/nsp12558A558FGCtTTt440.222222
ORF1ab/nsp12558A558CGCTTGC240.111111
ORF1ab/nsp12558A558CGCtTGt240.111111
ORF1ab/nsp12558A558PGctCct44All0.000001
ORF1ab/nsp12558A558FGCtTTt44All0.000001
ORF1ab/nsp12558A558CGCTTGC24All0
ORF1ab/nsp12558A558CGCtTGt24All0
ORF1ab/nsp12558A558AgcTgcC44AY.1030.000025
ORF1ab/nsp12558A558SGctTct44AY.1210.000541
ORF1ab/nsp12558A558SGctTct44B.1.617.20.000015
ORF1ab/nsp12558A558VgCtgTt330.166667
ORF1ab/nsp12558A558DgCtgAt33All0.000001
ORF1ab/nsp12558A558AgcTgcC33AY.1000.000138
ORF1ab/nsp12558A558AgcTgcC33AY.20.001068
ORF1ab/nsp12558A558SGctTct33AY.250.000018
ORF1ab/nsp12558A558delGCT---33AY.430.000013
ORF1ab/nsp12558A558AgcTgcA23AY.470.000062
ORF1ab/nsp12558A558AgcTgcC13AY.470.000031
ORF1ab/nsp12558A558AgcTgcC33AY.50.000062
ORF1ab/nsp12558A558VgCtgTt33B.10.000027
ORF1ab/nsp12558A558SGctTct33B.10.000027
ORF1ab/nsp12558A558VgCtgTt33B.1.10.000054
ORF1ab/nsp12558A558AgcTgcC33B.1.1.1890.004539
ORF1ab/nsp12558A558del1Gct-ct33B.1.177.820.001432
ORF1ab/nsp12558A558del1Gct-ct33B.1.3510.000089
ORF1ab/nsp12558A558AgcTgcC220.111111
ORF1ab/nsp12558A558AgcTgcC22AY.1020.000053
ORF1ab/nsp12558A558AgcTgcC22AY.1190.000071
ORF1ab/nsp12558A558SGctTct22AY.30.00002
ORF1ab/nsp12558A558delGCT---22AY.40.000003
ORF1ab/nsp12558A558SGctTct22AY.4.20.000043
ORF1ab/nsp12558A558AgcTgcC22AY.420.00008
ORF1ab/nsp12558A558SGctTct22AY.440.000012
ORF1ab/nsp12558A558SGctTct22AY.470.000062
ORF1ab/nsp12558A558AgcTgcA12AY.5.30.000337
ORF1ab/nsp12558A558AgcTgcC12AY.5.30.000337
ORF1ab/nsp12558A558del1Gct-ct22AY.520.001629
ORF1ab/nsp12558A558AgcTgcC22AY.75.10.000361
ORF1ab/nsp12558A558AgcTgcA22AY.99.20.000184
ORF1ab/nsp12558A558AgcTgcC22B.1.1.3060.000877
ORF1ab/nsp12558A558AgcTgcC22B.1.1.390.001019
ORF1ab/nsp12558A558del1Gct-ct22B.1.1600.000062
ORF1ab/nsp12558A558AgcTgcC22B.1.160.320.008584
ORF1ab/nsp12558A558AgcTgcC22B.1.3510.000059
ORF1ab/nsp12558A558AgcTgcA22B.1.5960.000174
ORF1ab/nsp12558A558delGCT---22P.10.000032
ORF1ab/nsp12558A558IGCtATt110.055556
ORF1ab/nsp12558A558SGctTct11A0.000387
ORF1ab/nsp12558A558SGctTct11A.2.50.000499
ORF1ab/nsp12558A558HGCtCAt11All0
ORF1ab/nsp12558A558IGCtATt11All0
ORF1ab/nsp12558A558YGCtTAt11All0
ORF1ab/nsp12558A558SGctTct11AY.100.00053
ORF1ab/nsp12558A558AgcTgcC11AY.1010.00049
ORF1ab/nsp12558A558SGctTct11AY.1020.000027
ORF1ab/nsp12558A558SGctTct11AY.1030.000006
ORF1ab/nsp12558A558VgCtgTt11AY.1030.000006
ORF1ab/nsp12558A558SGctTct11AY.1180.000063
ORF1ab/nsp12558A558AgcTgcC11AY.1180.000063
ORF1ab/nsp12558A558AgcTgcA11AY.160.00038
ORF1ab/nsp12558A558VgCtgTt11AY.200.000039
ORF1ab/nsp12558A558HGCtCAt11AY.250.000006
ORF1ab/nsp12558A558SGctTct11AY.290.000016
ORF1ab/nsp12558A558AgcTgcC11AY.29.10.000221
ORF1ab/nsp12558A558delGCT---11AY.30.00001
ORF1ab/nsp12558A558DgCtgAt11AY.30.00001
ORF1ab/nsp12558A558SGctTct11AY.330.000067
ORF1ab/nsp12558A558SGctTct11AY.390.000025
ORF1ab/nsp12558A558VgCtgTt11AY.390.000025
ORF1ab/nsp12558A558AgcTgcC11AY.39.10.00004
ORF1ab/nsp12558A558VgCTgTC11AY.40.000002
ORF1ab/nsp12558A558AgcTgcC11AY.4.20.000022
ORF1ab/nsp12558A558delGCT---11AY.420.00004
ORF1ab/nsp12558A558YGCtTAt11AY.440.000006
ORF1ab/nsp12558A558SGctTct11AY.460.000104
ORF1ab/nsp12558A558SGctTct11AY.50.000021
ORF1ab/nsp12558A558AgcTgcC11AY.550.000917
ORF1ab/nsp12558A558delGCT---11AY.590.00053
ORF1ab/nsp12558A558SGctTct11AY.60.000041
ORF1ab/nsp12558A558delGCT---11AY.650.000533
ORF1ab/nsp12558A558SGcTTcG11AY.670.000464
ORF1ab/nsp12558A558AgcTgcC11AY.710.000475
ORF1ab/nsp12558A558AgcTgcC11AY.770.001127
ORF1ab/nsp12558A558AgcTgcC11AY.790.001211
ORF1ab/nsp12558A558SGctTct11AY.840.000437
ORF1ab/nsp12558A558delGCT---11AY.840.000437
ORF1ab/nsp12558A558AgcTgcC11AY.9.20.000037
ORF1ab/nsp12558A558AgcTgcC11AY.910.00073
ORF1ab/nsp12558A558DgCtgAt11AY.920.000287
ORF1ab/nsp12558A558SGctTct11AY.980.000079
ORF1ab/nsp12558A558AgcTgcC11AY.98.10.000048
ORF1ab/nsp12558A558GgCTgGC11AY.990.001049
ORF1ab/nsp12558A558AgcTgcA11B0.000128
ORF1ab/nsp12558A558TGctAct11B.10.000009
ORF1ab/nsp12558A558DgCtgAt11B.10.000009
ORF1ab/nsp12558A558delGCT---11B.1.10.000018
ORF1ab/nsp12558A558SGctTct11B.1.1.10.000327
ORF1ab/nsp12558A558AgcTgcG11B.1.1.1300.015385
ORF1ab/nsp12558A558delGCT---11B.1.1.1390.022727
ORF1ab/nsp12558A558SGctTct11B.1.1.170.016667
ORF1ab/nsp12558A558SGctTct11B.1.1.1890.001513
ORF1ab/nsp12558A558VgCtgTt11B.1.1.250.000569
ORF1ab/nsp12558A558TGctAct11B.1.1.3720.000689
ORF1ab/nsp12558A558SGctTct11B.1.1.3740.002375
ORF1ab/nsp12558A558SGctTct11B.1.1.4090.002833
ORF1ab/nsp12558A558AgcTgcC11B.1.1.4150.05
ORF1ab/nsp12558A558SGctTct11B.1.1.5190.00004
ORF1ab/nsp12558A558VgCtgTt11B.1.1.70.000001
ORF1ab/nsp12558A558GgCtgGt11B.1.1.70.000001
ORF1ab/nsp12558A558PGctCct11B.1.1.70.000001
ORF1ab/nsp12558A558AgcTgcC11B.1.1.700.000341
ORF1ab/nsp12558A558VgCtgTt11B.1.160.160.000929
ORF1ab/nsp12558A558delGCT---11B.1.160.230.004831
ORF1ab/nsp12558A558TGctAct11B.1.1770.000013
ORF1ab/nsp12558A558del1Gct-ct11B.1.177.120.000152
ORF1ab/nsp12558A558AgcTgcC11B.1.177.120.000152
ORF1ab/nsp12558A558delGCT---11B.1.177.540.000606
ORF1ab/nsp12558A558del1Gct-ct11B.1.177.60.000977
ORF1ab/nsp12558A558delGCT---11B.1.177.680.015152
ORF1ab/nsp12558A558PGctCct11B.1.177.730.000566
ORF1ab/nsp12558A558VgCtgTt11B.1.177.90.001332
ORF1ab/nsp12558A558delGCT---11B.1.20.000009
ORF1ab/nsp12558A558PGctCct11B.1.20.000009
ORF1ab/nsp12558A558SGcTTcA11B.1.20.000009
ORF1ab/nsp12558A558AgcTgcC11B.1.2210.000071
ORF1ab/nsp12558A558VgCtgTt11B.1.2430.00007
ORF1ab/nsp12558A558SGctTct11B.1.2430.00007
ORF1ab/nsp12558A558SGctTct11B.1.3510.00003
ORF1ab/nsp12558A558SGctTct11B.1.360.000146
ORF1ab/nsp12558A558del1Gct-ct11B.1.36.10.00114
ORF1ab/nsp12558A558PGctCct11B.1.36.360.000602
ORF1ab/nsp12558A558TGcTAcA11B.1.4160.001269
ORF1ab/nsp12558A558AgcTgcA11B.1.4160.001269
ORF1ab/nsp12558A558AgcTgcC11B.1.4290.000024
ORF1ab/nsp12558A558GgCtgGt11B.1.438.10.000107
ORF1ab/nsp12558A558AgcTgcA11B.1.4620.007246
ORF1ab/nsp12558A558AgcTgcC11B.1.5170.000427
ORF1ab/nsp12558A558SGctTct11B.1.5230.002451
ORF1ab/nsp12558A558AgcTgcC11B.1.5260.000024
ORF1ab/nsp12558A558AgcTgcC11B.1.5820.000491
ORF1ab/nsp12558A558AgcTgcC11B.1.5990.00365
ORF1ab/nsp12558A558AgcTgcC11B.1.617.10.000129
ORF1ab/nsp12558A558SGctTct11B.1.617.10.000129
ORF1ab/nsp12558A558VgCtgTt11B.1.617.20.000004
ORF1ab/nsp12558A558TGctAct11B.1.6250.002353
ORF1ab/nsp12558A558AgcTgcC11B.1.6280.000352
ORF1ab/nsp12558A558AgcTgcA11B.1.6360.006711
ORF1ab/nsp12558A558SGctTct11B.340.013699
ORF1ab/nsp12558A558AgcTgcC11P.10.000016
ORF1ab/nsp12558A558AgcTgcC11P.1.100.000269
ORF1ab/nsp12558A558del1gCtg-t11P.1.10.10.00813
ORF1ab/nsp12558A558delGCT---11P.1.40.000977
ORF1ab/nsp12558A558AgcTgcA11P.1.70.000319
ORF1ab/nsp12558A558delGCT---11Q.20.000613
ORF1ab/nsp12558A558del1Gct-ct11R.10.00009

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.