CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 101

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/nsp4101F101LF2864LnonsynTttCtt8848440.9547518855-8857
ORF1ab/nsp4101F101LF2864LnonsynttTttA884290.03280548855-8857
ORF1ab/nsp4101F101LF2864LnonsynttTttG884100.01131228855-8857
ORF1ab/nsp4101F101LF2864LnonsynTtTCtG88410.001131228855-8857
ORF1ab/nsp4101F101FF2864FsynttTttC17117118855-8857
ORF1ab/nsp4101F101delF2864deldelTTT---12512518855-8857
ORF1ab/nsp4101F101SF2864SnonsyntTttCt48470.9791678855-8857
ORF1ab/nsp4101F101SF2864SnonsyntTTtCA4810.02083338855-8857
ORF1ab/nsp4101F101YF2864YnonsyntTttAt242418855-8857
ORF1ab/nsp4101F101IF2864InonsynTttAtt222218855-8857
ORF1ab/nsp4101F101CF2864CnonsyntTttGt222218855-8857
ORF1ab/nsp4101F101VF2864VnonsynTttGtt131318855-8857
ORF1ab/nsp4101F101del1F2864del1delTtt-tt210.58855-8857
ORF1ab/nsp4101F101del1F2864del1delttTtt-210.58855-8857
ORF1ab/nsp4101F101NF2864NnonsynTTtAAt1118855-8857
ORF1ab/nsp4101F101del2F2864del2delTTt--t1118855-8857
ORF1ab/nsp4101F101GF2864GnonsynTTTGGG1118855-8857
ORF1ab/nsp4101F101PF2864PnonsynTTTCCG1118855-8857

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/nsp4101F101LTttCtt844884All0.000161
ORF1ab/nsp4101F101LttTttA29884All0.000006
ORF1ab/nsp4101F101LttTttG10884All0.000002
ORF1ab/nsp4101F101LTtTCtG1884All0
ORF1ab/nsp4101F101LTttCtt535540B.1.1.70.000479
ORF1ab/nsp4101F101LttTttA5540B.1.1.70.000004
ORF1ab/nsp4101F101FttTttC171171All0.000033
ORF1ab/nsp4101F101LTttCtt168168B.1.1.2040.510638
ORF1ab/nsp4101F101delTTT---125125All0.000024
ORF1ab/nsp4101F101FttTttC6565AY.460.006765
ORF1ab/nsp4101F101StTttCt4748All0.000009
ORF1ab/nsp4101F101StTTtCA148All0
ORF1ab/nsp4101F101delTTT---4444B.1.1.70.000039
ORF1ab/nsp4101F101LTttCtt3536B.1.617.20.000132
ORF1ab/nsp4101F101LttTttA136B.1.617.20.000004
ORF1ab/nsp4101F101YtTttAt2424All0.000005
ORF1ab/nsp4101F101CtTttGt2222All0.000004
ORF1ab/nsp4101F101ITttAtt2222All0.000004
ORF1ab/nsp4101F101LTttCtt2121B.1.5260.000494
ORF1ab/nsp4101F101FttTttC2020AY.40.000031
ORF1ab/nsp4101F101LttTttA1018AY.40.000016
ORF1ab/nsp4101F101LTttCtt818AY.40.000012
ORF1ab/nsp4101F101YtTttAt1717B.1.1.70.000015
ORF1ab/nsp4101F101StTttCt1616B.1.1.70.000014
ORF1ab/nsp4101F101StTttCt1515B.1.1600.000468
ORF1ab/nsp4101F101CtTttGt1414B.1.2580.000932
ORF1ab/nsp4101F101VTttGtt1313All0.000002
ORF1ab/nsp4101F101FttTttC1212AY.440.000073
ORF1ab/nsp4101F101LTttCtt912B.1.20.000079
ORF1ab/nsp4101F101LttTttA212B.1.20.000018
ORF1ab/nsp4101F101LttTttG112B.1.20.000009
ORF1ab/nsp4101F101FttTttC1212B.1.2210.000852
ORF1ab/nsp4101F101delTTT---1111AY.430.000049
ORF1ab/nsp4101F101delTTT---1010AY.40.000016
ORF1ab/nsp4101F101FttTttC99AY.1030.000056
ORF1ab/nsp4101F101FttTttC99B.1.1.70.000008
ORF1ab/nsp4101F101FttTttC99B.1.617.20.000034
ORF1ab/nsp4101F101delTTT---88B.1.1770.000105
ORF1ab/nsp4101F101LTttCtt77AY.1060.002344
ORF1ab/nsp4101F101LTttCtt66AY.3.10.000512
ORF1ab/nsp4101F101ITttAtt66AY.430.000027
ORF1ab/nsp4101F101LTttCtt66B.1.5960.000523
ORF1ab/nsp4101F101ITttAtt66B.1.617.20.000023
ORF1ab/nsp4101F101LTttCtt46P.10.000063
ORF1ab/nsp4101F101LttTttG16P.10.000016
ORF1ab/nsp4101F101LTtTCtG16P.10.000016
ORF1ab/nsp4101F101LTttCtt55AY.230.000349
ORF1ab/nsp4101F101delTTT---55AY.4.50.000537
ORF1ab/nsp4101F101LttTttA25AY.430.000009
ORF1ab/nsp4101F101LTttCtt25AY.430.000009
ORF1ab/nsp4101F101LttTttG15AY.430.000004
ORF1ab/nsp4101F101LTttCtt55B.1.36.80.005
ORF1ab/nsp4101F101FttTttC55P.10.000079
ORF1ab/nsp4101F101delTTT---44B.10.000037
ORF1ab/nsp4101F101LttTttG44B.1.10.000073
ORF1ab/nsp4101F101LTttCtt33AU.20.007264
ORF1ab/nsp4101F101LTttCtt33AY.390.000074
ORF1ab/nsp4101F101ITttAtt33AY.40.000005
ORF1ab/nsp4101F101FttTttC33B.10.000027
ORF1ab/nsp4101F101FttTttC33B.1.1600.000094
ORF1ab/nsp4101F101VTttGtt33B.1.1770.00004
ORF1ab/nsp4101F101LTttCtt33P.30.004785
ORF1ab/nsp4101F101LttTttG220.111111
ORF1ab/nsp4101F101delTTT---220.111111
ORF1ab/nsp4101F101delTTT---22A.20.001324
ORF1ab/nsp4101F101del1Ttt-tt12All0
ORF1ab/nsp4101F101del1ttTtt-12All0
ORF1ab/nsp4101F101FttTttC22AY.1020.000053
ORF1ab/nsp4101F101LTttCtt22AY.1030.000012
ORF1ab/nsp4101F101LttTttA22AY.130.000322
ORF1ab/nsp4101F101StTttCt22AY.250.000012
ORF1ab/nsp4101F101delTTT---22AY.250.000012
ORF1ab/nsp4101F101LTttCtt22AY.30.00002
ORF1ab/nsp4101F101StTttCt22AY.40.000003
ORF1ab/nsp4101F101LTttCtt22AY.4.20.000043
ORF1ab/nsp4101F101StTttCt22AY.430.000009
ORF1ab/nsp4101F101StTttCt22AY.470.000062
ORF1ab/nsp4101F101LTttCtt12AY.540.000095
ORF1ab/nsp4101F101LttTttA12AY.540.000095
ORF1ab/nsp4101F101FttTttC22AY.570.001312
ORF1ab/nsp4101F101CtTttGt22AY.9.20.000073
ORF1ab/nsp4101F101LTttCtt22B0.000256
ORF1ab/nsp4101F101StTttCt12B.10.000009
ORF1ab/nsp4101F101StTTtCA12B.10.000009
ORF1ab/nsp4101F101FttTttC22B.1.1.5190.000079
ORF1ab/nsp4101F101FttTttC22B.1.1770.000026
ORF1ab/nsp4101F101LttTttA22B.1.177.100.001756
ORF1ab/nsp4101F101delTTT---22B.1.20.000018
ORF1ab/nsp4101F101delTTT---22B.1.36.170.000988
ORF1ab/nsp4101F101LTttCtt22B.1.466.20.000782
ORF1ab/nsp4101F101VTttGtt22B.1.617.20.000008
ORF1ab/nsp4101F101ITttAtt22B.1.6210.000177
ORF1ab/nsp4101F101ITttAtt110.055556
ORF1ab/nsp4101F101delTTT---11AH.30.003802
ORF1ab/nsp4101F101del2TTt--t11All0
ORF1ab/nsp4101F101PTTTCCG11All0
ORF1ab/nsp4101F101NTTtAAt11All0
ORF1ab/nsp4101F101GTTTGGG11All0
ORF1ab/nsp4101F101FttTttC11AY.1000.000046
ORF1ab/nsp4101F101CtTttGt11AY.1030.000006
ORF1ab/nsp4101F101delTTT---11AY.1110.000183
ORF1ab/nsp4101F101FttTttC11AY.1130.000142
ORF1ab/nsp4101F101YtTttAt11AY.1170.000085
ORF1ab/nsp4101F101delTTT---11AY.1200.000037
ORF1ab/nsp4101F101delTTT---11AY.190.00114
ORF1ab/nsp4101F101CtTttGt11AY.190.00114
ORF1ab/nsp4101F101VTttGtt11AY.230.00007
ORF1ab/nsp4101F101FttTttC11AY.230.00007
ORF1ab/nsp4101F101LTttCtt11AY.240.000431
ORF1ab/nsp4101F101FttTttC11AY.240.000431
ORF1ab/nsp4101F101ITttAtt11AY.250.000006
ORF1ab/nsp4101F101FttTttC11AY.250.000006
ORF1ab/nsp4101F101YtTttAt11AY.260.000028
ORF1ab/nsp4101F101FttTttC11AY.260.000028
ORF1ab/nsp4101F101StTttCt11AY.290.000016
ORF1ab/nsp4101F101FttTttC11AY.30.00001
ORF1ab/nsp4101F101delTTT---11AY.330.000067
ORF1ab/nsp4101F101VTttGtt11AY.40.000002
ORF1ab/nsp4101F101CtTttGt11AY.40.000002
ORF1ab/nsp4101F101YtTttAt11AY.40.000002
ORF1ab/nsp4101F101del2TTt--t11AY.40.000002
ORF1ab/nsp4101F101StTttCt11AY.4.2.10.000149
ORF1ab/nsp4101F101VTttGtt11AY.420.00004
ORF1ab/nsp4101F101FttTttC11AY.430.000004
ORF1ab/nsp4101F101LttTttA11AY.440.000006
ORF1ab/nsp4101F101YtTttAt11AY.440.000006
ORF1ab/nsp4101F101delTTT---11AY.450.000122
ORF1ab/nsp4101F101FttTttC11AY.46.60.000072
ORF1ab/nsp4101F101FttTttC11AY.50.000021
ORF1ab/nsp4101F101delTTT---11AY.50.000021
ORF1ab/nsp4101F101CtTttGt11AY.60.000041
ORF1ab/nsp4101F101del1ttTtt-11AY.600.000938
ORF1ab/nsp4101F101FttTttC11AY.610.000105
ORF1ab/nsp4101F101LttTttA11AY.690.000187
ORF1ab/nsp4101F101VTttGtt11AY.690.000187
ORF1ab/nsp4101F101delTTT---11AY.720.001361
ORF1ab/nsp4101F101LTttCtt11AY.740.000116
ORF1ab/nsp4101F101LTttCtt11AY.750.000056
ORF1ab/nsp4101F101delTTT---11AY.90.000068
ORF1ab/nsp4101F101delTTT---11AY.9.20.000037
ORF1ab/nsp4101F101VTttGtt11AY.9.20.000037
ORF1ab/nsp4101F101YtTttAt11AY.990.001049
ORF1ab/nsp4101F101delTTT---11AY.99.10.001553
ORF1ab/nsp4101F101LttTttA11B.10.000009
ORF1ab/nsp4101F101ITttAtt11B.10.000009
ORF1ab/nsp4101F101delTTT---11B.1.10.000018
ORF1ab/nsp4101F101CtTttGt11B.1.10.000018
ORF1ab/nsp4101F101LttTttG11B.1.1.1210.002427
ORF1ab/nsp4101F101LTttCtt11B.1.1.1330.008475
ORF1ab/nsp4101F101delTTT---11B.1.1.3060.000438
ORF1ab/nsp4101F101PTTTCCG11B.1.1.3060.000438
ORF1ab/nsp4101F101delTTT---11B.1.1.3110.000358
ORF1ab/nsp4101F101delTTT---11B.1.1.3150.008475
ORF1ab/nsp4101F101delTTT---11B.1.1.4090.002833
ORF1ab/nsp4101F101FttTttC11B.1.1.4320.001266
ORF1ab/nsp4101F101FttTttC11B.1.1.5230.001563
ORF1ab/nsp4101F101CtTttGt11B.1.1.70.000001
ORF1ab/nsp4101F101delTTT---11B.1.1.700.000341
ORF1ab/nsp4101F101LTttCtt11B.1.1040.00369
ORF1ab/nsp4101F101delTTT---11B.1.1400.018868
ORF1ab/nsp4101F101LTttCtt11B.1.160.220.006757
ORF1ab/nsp4101F101delTTT---11B.1.160.230.004831
ORF1ab/nsp4101F101StTttCt11B.1.1770.000013
ORF1ab/nsp4101F101delTTT---11B.1.177.160.000664
ORF1ab/nsp4101F101delTTT---11B.1.177.190.001431
ORF1ab/nsp4101F101delTTT---11B.1.177.550.002331
ORF1ab/nsp4101F101delTTT---11B.1.177.570.000281
ORF1ab/nsp4101F101delTTT---11B.1.177.620.001192
ORF1ab/nsp4101F101delTTT---11B.1.177.630.002703
ORF1ab/nsp4101F101delTTT---11B.1.177.690.001484
ORF1ab/nsp4101F101VTttGtt11B.1.2100.002132
ORF1ab/nsp4101F101delTTT---11B.1.221.10.002907
ORF1ab/nsp4101F101NTTtAAt11B.1.221.40.004167
ORF1ab/nsp4101F101LttTttA11B.1.2430.00007
ORF1ab/nsp4101F101delTTT---11B.1.258.110.000396
ORF1ab/nsp4101F101VTttGtt11B.1.3510.00003
ORF1ab/nsp4101F101StTttCt11B.1.3820.008929
ORF1ab/nsp4101F101FttTttC11B.1.3830.009009
ORF1ab/nsp4101F101FttTttC11B.1.3910.001127
ORF1ab/nsp4101F101YtTttAt11B.1.3960.000706
ORF1ab/nsp4101F101StTttCt11B.1.4000.000429
ORF1ab/nsp4101F101LTttCtt11B.1.4290.000024
ORF1ab/nsp4101F101del1Ttt-tt11B.1.4290.000024
ORF1ab/nsp4101F101YtTttAt11B.1.466.20.000391
ORF1ab/nsp4101F101GTTTGGG11B.1.466.20.000391
ORF1ab/nsp4101F101StTttCt11B.1.5260.000024
ORF1ab/nsp4101F101ITttAtt11B.1.5260.000024
ORF1ab/nsp4101F101StTttCt11B.1.5630.016949
ORF1ab/nsp4101F101delTTT---11B.1.5960.000087
ORF1ab/nsp4101F101LTttCtt11B.1.5990.00365
ORF1ab/nsp4101F101LTttCtt11B.1.617.10.000129
ORF1ab/nsp4101F101delTTT---11B.1.617.10.000129
ORF1ab/nsp4101F101LTttCtt11B.1.6210.000089
ORF1ab/nsp4101F101delTTT---11B.150.017544
ORF1ab/nsp4101F101LTttCtt11B.60.00091
ORF1ab/nsp4101F101VTttGtt11C.350.000774
ORF1ab/nsp4101F101LTttCtt11C.370.000116
ORF1ab/nsp4101F101LTttCtt11D.20.000075
ORF1ab/nsp4101F101delTTT---11P.10.000016
ORF1ab/nsp4101F101FttTttC11P.1.140.000048
ORF1ab/nsp4101F101ITttAtt11Q.10.000126
ORF1ab/nsp4101F101delTTT---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.