CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1776

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/nsp31776Y1776YY2594YsyntaCtaT334703347018045-8047
ORF1ab/nsp31776Y1776delY2594deldelTAC---11811818045-8047
ORF1ab/nsp31776Y1776HY2594HnonsynTacCac434318045-8047
ORF1ab/nsp31776Y1776FY2594FnonsyntActTc3318045-8047
ORF1ab/nsp31776Y1776XY2594XnonsyntaCtaG320.6666678045-8047
ORF1ab/nsp31776Y1776CY2594CnonsyntActGc320.6666678045-8047
ORF1ab/nsp31776Y1776CY2594CnonsyntACtGT310.3333338045-8047
ORF1ab/nsp31776Y1776XY2594XnonsyntaCtaA310.3333338045-8047
ORF1ab/nsp31776Y1776del1Y2594del1deltaCta-2218045-8047
ORF1ab/nsp31776Y1776del2Y2594del2deltACt--1118045-8047
ORF1ab/nsp31776Y1776NY2594NnonsynTacAac1118045-8047
ORF1ab/nsp31776Y1776DY2594DnonsynTacGac1118045-8047

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/nsp31776Y1776YtaCtaT3347033470All0.006402
ORF1ab/nsp31776Y1776YtaCtaT1472814728B.1.2580.980102
ORF1ab/nsp31776Y1776YtaCtaT95779577B.1.258.170.995737
ORF1ab/nsp31776Y1776YtaCtaT25162516B.1.258.110.997226
ORF1ab/nsp31776Y1776YtaCtaT10201020B.1.258.141
ORF1ab/nsp31776Y1776YtaCtaT611611B.1.258.161
ORF1ab/nsp31776Y1776YtaCtaT597597B.1.258.31
ORF1ab/nsp31776Y1776YtaCtaT523523B.1.258.71
ORF1ab/nsp31776Y1776YtaCtaT482482B.1.1.70.000431
ORF1ab/nsp31776Y1776YtaCtaT375375B.1.258.221
ORF1ab/nsp31776Y1776YtaCtaT290290B.1.258.41
ORF1ab/nsp31776Y1776YtaCtaT258258B.10.002363
ORF1ab/nsp31776Y1776YtaCtaT243243B.1.4270.012271
ORF1ab/nsp31776Y1776YtaCtaT222222B.1.258.21
ORF1ab/nsp31776Y1776YtaCtaT200200B.1.258.91
ORF1ab/nsp31776Y1776YtaCtaT141141B.1.258.191
ORF1ab/nsp31776Y1776YtaCtaT127127B.1.258.121
ORF1ab/nsp31776Y1776YtaCtaT127127B.1.258.210.984496
ORF1ab/nsp31776Y1776delTAC---118118All0.000023
ORF1ab/nsp31776Y1776YtaCtaT114114B.1.258.51
ORF1ab/nsp31776Y1776YtaCtaT9696B.1.617.20.000361
ORF1ab/nsp31776Y1776YtaCtaT9393B.1.258.241
ORF1ab/nsp31776Y1776YtaCtaT8888B.1.258.101
ORF1ab/nsp31776Y1776YtaCtaT6767B.1.10.001215
ORF1ab/nsp31776Y1776YtaCtaT6363B.1.258.201
ORF1ab/nsp31776Y1776YtaCtaT5353B.1.258.151
ORF1ab/nsp31776Y1776YtaCtaT5252P.10.000819
ORF1ab/nsp31776Y1776YtaCtaT5151B.1.258.61
ORF1ab/nsp31776Y1776YtaCtaT5050B.1.1770.000658
ORF1ab/nsp31776Y1776delTAC---4646B.1.1.70.000041
ORF1ab/nsp31776Y1776HTacCac4343All0.000008
ORF1ab/nsp31776Y1776YtaCtaT4242B.1.258.231
ORF1ab/nsp31776Y1776YtaCtaT3737AY.1030.00023
ORF1ab/nsp31776Y1776YtaCtaT3636AY.40.000056
ORF1ab/nsp31776Y1776YtaCtaT3232AY.200.001244
ORF1ab/nsp31776Y1776YtaCtaT3131AY.250.000186
ORF1ab/nsp31776Y1776YtaCtaT3030R.10.0027
ORF1ab/nsp31776Y1776HTacCac2828AY.40.000044
ORF1ab/nsp31776Y1776YtaCtaT2828B.1.1600.000873
ORF1ab/nsp31776Y1776YtaCtaT2727B.1.6090.012943
ORF1ab/nsp31776Y1776YtaCtaT2424AY.440.000146
ORF1ab/nsp31776Y1776YtaCtaT2323G.10.958333
ORF1ab/nsp31776Y1776YtaCtaT2222AY.260.000623
ORF1ab/nsp31776Y1776YtaCtaT1919AY.1000.000874
ORF1ab/nsp31776Y1776YtaCtaT1919B.1.2210.00135
ORF1ab/nsp31776Y1776YtaCtaT1818AY.430.00008
ORF1ab/nsp31776Y1776YtaCtaT1616AY.39.10.000634
ORF1ab/nsp31776Y1776YtaCtaT1515AY.1060.005023
ORF1ab/nsp31776Y1776YtaCtaT1515B.1.3670.011886
ORF1ab/nsp31776Y1776YtaCtaT1414B.1.5750.004248
ORF1ab/nsp31776Y1776YtaCtaT1313B.1.1.5190.000516
ORF1ab/nsp31776Y1776delTAC---1111AY.40.000017
ORF1ab/nsp31776Y1776YtaCtaT1010B.1.258.181
ORF1ab/nsp31776Y1776YtaCtaT1010B.1.6000.05848
ORF1ab/nsp31776Y1776YtaCtaT99AY.20.003205
ORF1ab/nsp31776Y1776YtaCtaT99AY.30.00009
ORF1ab/nsp31776Y1776YtaCtaT88A0.003096
ORF1ab/nsp31776Y1776delTAC---77B.10.000064
ORF1ab/nsp31776Y1776YtaCtaT77B.4.10.132075
ORF1ab/nsp31776Y1776YtaCtaT77C.10.016746
ORF1ab/nsp31776Y1776YtaCtaT66B.1.20.000053
ORF1ab/nsp31776Y1776delTAC---55B.1.10.000091
ORF1ab/nsp31776Y1776delTAC---55B.1.1770.000066
ORF1ab/nsp31776Y1776YtaCtaT55B.1.177.810.000947
ORF1ab/nsp31776Y1776YtaCtaT55B.1.360.00073
ORF1ab/nsp31776Y1776YtaCtaT55B.1.3750.004098
ORF1ab/nsp31776Y1776YtaCtaT55B.1.4110.018519
ORF1ab/nsp31776Y1776YtaCtaT55C.370.00058
ORF1ab/nsp31776Y1776delTAC---44AY.250.000024
ORF1ab/nsp31776Y1776delTAC---44AY.4.50.00043
ORF1ab/nsp31776Y1776YtaCtaT44AY.46.20.002541
ORF1ab/nsp31776Y1776HTacCac44B.1.1.70.000004
ORF1ab/nsp31776Y1776YtaCtaT44B.1.3510.000119
ORF1ab/nsp31776Y1776YtaCtaT44C.360.003643
ORF1ab/nsp31776Y1776FtActTc33All0.000001
ORF1ab/nsp31776Y1776XtaCtaG23All0
ORF1ab/nsp31776Y1776CtActGc23All0
ORF1ab/nsp31776Y1776CtACtGT13All0
ORF1ab/nsp31776Y1776XtaCtaA13All0
ORF1ab/nsp31776Y1776YtaCtaT33AY.1020.00008
ORF1ab/nsp31776Y1776YtaCtaT33AY.4.20.000065
ORF1ab/nsp31776Y1776YtaCtaT33AY.420.000121
ORF1ab/nsp31776Y1776delTAC---33AY.430.000013
ORF1ab/nsp31776Y1776YtaCtaT33AY.9.20.00011
ORF1ab/nsp31776Y1776YtaCtaT33B0.000383
ORF1ab/nsp31776Y1776YtaCtaT33B.1.1.3010.003538
ORF1ab/nsp31776Y1776YtaCtaT33B.1.1.700.001023
ORF1ab/nsp31776Y1776YtaCtaT33B.1.177.60.00293
ORF1ab/nsp31776Y1776YtaCtaT33B.1.177.730.001699
ORF1ab/nsp31776Y1776YtaCtaT33B.1.177.880.037037
ORF1ab/nsp31776Y1776YtaCtaT33B.1.2220.005076
ORF1ab/nsp31776Y1776YtaCtaT33P.1.10.000953
ORF1ab/nsp31776Y1776YtaCtaT33P.1.120.001452
ORF1ab/nsp31776Y1776del1taCta-22All0
ORF1ab/nsp31776Y1776YtaCtaT22AY.230.000139
ORF1ab/nsp31776Y1776YtaCtaT22AY.270.000129
ORF1ab/nsp31776Y1776YtaCtaT22AY.290.000032
ORF1ab/nsp31776Y1776YtaCtaT22AY.330.000134
ORF1ab/nsp31776Y1776del1taCta-22AY.40.000003
ORF1ab/nsp31776Y1776YtaCtaT22AY.460.000208
ORF1ab/nsp31776Y1776YtaCtaT22AY.470.000062
ORF1ab/nsp31776Y1776YtaCtaT22AY.540.000191
ORF1ab/nsp31776Y1776YtaCtaT22AY.650.001066
ORF1ab/nsp31776Y1776YtaCtaT22AY.880.001768
ORF1ab/nsp31776Y1776YtaCtaT22B.1.1.1530.002191
ORF1ab/nsp31776Y1776delTAC---22B.1.1.3150.016949
ORF1ab/nsp31776Y1776YtaCtaT22B.1.1.390.001019
ORF1ab/nsp31776Y1776YtaCtaT22B.1.1.4240.090909
ORF1ab/nsp31776Y1776YtaCtaT22B.1.1.4340.000697
ORF1ab/nsp31776Y1776delTAC---22B.1.1.460.008734
ORF1ab/nsp31776Y1776FtActTc22B.1.1.70.000002
ORF1ab/nsp31776Y1776YtaCtaT22B.1.177.40.000422
ORF1ab/nsp31776Y1776YtaCtaT22B.1.177.70.00033
ORF1ab/nsp31776Y1776YtaCtaT22B.1.177.860.000367
ORF1ab/nsp31776Y1776HTacCac22B.1.20.000018
ORF1ab/nsp31776Y1776YtaCtaT22B.1.2400.000431
ORF1ab/nsp31776Y1776YtaCtaT22B.1.4290.000047
ORF1ab/nsp31776Y1776YtaCtaT22B.1.4320.022472
ORF1ab/nsp31776Y1776YtaCtaT22B.1.5260.000047
ORF1ab/nsp31776Y1776HTacCac22B.1.617.20.000008
ORF1ab/nsp31776Y1776YtaCtaT22C.110.021277
ORF1ab/nsp31776Y1776YtaCtaT110.055556
ORF1ab/nsp31776Y1776YtaCtaT11A.2.50.000499
ORF1ab/nsp31776Y1776YtaCtaT11AA.10.007246
ORF1ab/nsp31776Y1776NTacAac11All0
ORF1ab/nsp31776Y1776DTacGac11All0
ORF1ab/nsp31776Y1776del2tACt--11All0
ORF1ab/nsp31776Y1776delTAC---11AY.1030.000006
ORF1ab/nsp31776Y1776YtaCtaT11AY.1090.00074
ORF1ab/nsp31776Y1776delTAC---11AY.1110.000183
ORF1ab/nsp31776Y1776YtaCtaT11AY.1180.000063
ORF1ab/nsp31776Y1776delTAC---11AY.1190.000035
ORF1ab/nsp31776Y1776YtaCtaT11AY.240.000431
ORF1ab/nsp31776Y1776YtaCtaT11AY.320.000532
ORF1ab/nsp31776Y1776delTAC---11AY.330.000067
ORF1ab/nsp31776Y1776YtaCtaT11AY.390.000025
ORF1ab/nsp31776Y1776FtActTc11AY.40.000002
ORF1ab/nsp31776Y1776YtaCtaT11AY.4.2.10.000149
ORF1ab/nsp31776Y1776YtaCtaT11AY.4.50.000107
ORF1ab/nsp31776Y1776HTacCac11AY.420.00004
ORF1ab/nsp31776Y1776HTacCac11AY.430.000004
ORF1ab/nsp31776Y1776delTAC---11AY.46.20.000635
ORF1ab/nsp31776Y1776YtaCtaT11AY.50.000021
ORF1ab/nsp31776Y1776YtaCtaT11AY.520.000814
ORF1ab/nsp31776Y1776YtaCtaT11AY.610.000105
ORF1ab/nsp31776Y1776YtaCtaT11AY.620.000436
ORF1ab/nsp31776Y1776delTAC---11AY.720.001361
ORF1ab/nsp31776Y1776delTAC---11AY.750.000056
ORF1ab/nsp31776Y1776HTacCac11AY.750.000056
ORF1ab/nsp31776Y1776YtaCtaT11AY.760.004831
ORF1ab/nsp31776Y1776YtaCtaT11AY.790.001211
ORF1ab/nsp31776Y1776YtaCtaT11AY.840.000437
ORF1ab/nsp31776Y1776YtaCtaT11AY.90.000068
ORF1ab/nsp31776Y1776YtaCtaT11AY.950.000761
ORF1ab/nsp31776Y1776XtaCtaG11AY.970.001701
ORF1ab/nsp31776Y1776YtaCtaT11AY.980.000079
ORF1ab/nsp31776Y1776YtaCtaT11AY.98.10.000048
ORF1ab/nsp31776Y1776CtActGc11B.10.000009
ORF1ab/nsp31776Y1776XtaCtaA11B.10.000009
ORF1ab/nsp31776Y1776HTacCac11B.10.000009
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.10.000327
ORF1ab/nsp31776Y1776HTacCac11B.1.1.1190.034483
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.1230.017857
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.1610.003534
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.1980.001468
ORF1ab/nsp31776Y1776delTAC---11B.1.1.2360.006897
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.2860.002899
ORF1ab/nsp31776Y1776delTAC---11B.1.1.3060.000438
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.3060.000438
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.3110.000358
ORF1ab/nsp31776Y1776delTAC---11B.1.1.3110.000358
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.3690.000446
ORF1ab/nsp31776Y1776delTAC---11B.1.1.370.000193
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.3720.000689
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.4090.002833
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.4160.000905
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.510.001718
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1.630.000386
ORF1ab/nsp31776Y1776del2tACt--11B.1.1.70.000001
ORF1ab/nsp31776Y1776delTAC---11B.1.1.700.000341
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1390.000733
ORF1ab/nsp31776Y1776delTAC---11B.1.1400.018868
ORF1ab/nsp31776Y1776YtaCtaT11B.1.1570.002985
ORF1ab/nsp31776Y1776delTAC---11B.1.177.160.000664
ORF1ab/nsp31776Y1776delTAC---11B.1.177.180.00116
ORF1ab/nsp31776Y1776YtaCtaT11B.1.177.450.000381
ORF1ab/nsp31776Y1776YtaCtaT11B.1.177.50.001242
ORF1ab/nsp31776Y1776delTAC---11B.1.177.60.000977
ORF1ab/nsp31776Y1776delTAC---11B.1.177.620.001192
ORF1ab/nsp31776Y1776YtaCtaT11B.1.177.830.001481
ORF1ab/nsp31776Y1776CtActGc11B.1.20.000009
ORF1ab/nsp31776Y1776DTacGac11B.1.20.000009
ORF1ab/nsp31776Y1776YtaCtaT11B.1.221.30.000833
ORF1ab/nsp31776Y1776delTAC---11B.1.2420.018868
ORF1ab/nsp31776Y1776YtaCtaT11B.1.2430.00007
ORF1ab/nsp31776Y1776YtaCtaT11B.1.2470.014925
ORF1ab/nsp31776Y1776delTAC---11B.1.258.110.000396
ORF1ab/nsp31776Y1776YtaCtaT11B.1.2930.0125
ORF1ab/nsp31776Y1776YtaCtaT11B.1.3010.005917
ORF1ab/nsp31776Y1776delTAC---11B.1.36.180.00042
ORF1ab/nsp31776Y1776YtaCtaT11B.1.3690.000285
ORF1ab/nsp31776Y1776YtaCtaT11B.1.3910.001127
ORF1ab/nsp31776Y1776YtaCtaT11B.1.4060.006061
ORF1ab/nsp31776Y1776HTacCac11B.1.4270.00005
ORF1ab/nsp31776Y1776HTacCac11B.1.4290.000024
ORF1ab/nsp31776Y1776YtaCtaT11B.1.5240.001406
ORF1ab/nsp31776Y1776YtaCtaT11B.1.5760.000907
ORF1ab/nsp31776Y1776YtaCtaT11B.1.5960.000087
ORF1ab/nsp31776Y1776delTAC---11B.1.617.20.000004
ORF1ab/nsp31776Y1776XtaCtaG11B.1.617.20.000004
ORF1ab/nsp31776Y1776CtACtGT11B.1.617.20.000004
ORF1ab/nsp31776Y1776YtaCtaT11B.1.6210.000089
ORF1ab/nsp31776Y1776YtaCtaT11B.1.6230.000536
ORF1ab/nsp31776Y1776YtaCtaT11B.1.6270.00202
ORF1ab/nsp31776Y1776delTAC---11B.1.6380.052632
ORF1ab/nsp31776Y1776YtaCtaT11C.140.004329
ORF1ab/nsp31776Y1776YtaCtaT11C.230.005814
ORF1ab/nsp31776Y1776delTAC---11C.350.000774
ORF1ab/nsp31776Y1776delTAC---11C.370.000116
ORF1ab/nsp31776Y1776YtaCtaT11D.20.000075
ORF1ab/nsp31776Y1776NTacAac11D.20.000075
ORF1ab/nsp31776Y1776delTAC---11P.10.000016
ORF1ab/nsp31776Y1776YtaCtaT11P.1.140.000048
ORF1ab/nsp31776Y1776YtaCtaT11P.1.150.000232
ORF1ab/nsp31776Y1776delTAC---11P.1.150.000232
ORF1ab/nsp31776Y1776YtaCtaT11P.20.000187
ORF1ab/nsp31776Y1776YtaCtaT11P.30.001595
ORF1ab/nsp31776Y1776delTAC---11Q.10.000126
ORF1ab/nsp31776Y1776delTAC---11Q.20.000613
ORF1ab/nsp31776Y1776YtaCtaT11Q.80.000165
ORF1ab/nsp31776Y1776delTAC---11U.30.003861

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.