CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 499

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/nsp2499F499LF679LnonsynTttCtt4634100.8855292300-2302
ORF1ab/nsp2499F499LF679LnonsynttTttA463350.0755942300-2302
ORF1ab/nsp2499F499LF679LnonsynttTttG463130.02807782300-2302
ORF1ab/nsp2499F499LF679LnonsynTtTCtG46330.006479482300-2302
ORF1ab/nsp2499F499LF679LnonsynTtTCtA46320.004319652300-2302
ORF1ab/nsp2499F499FF679FsynttTttC11211212300-2302
ORF1ab/nsp2499F499delF679deldelTTT---747412300-2302
ORF1ab/nsp2499F499SF679SnonsyntTttCt73700.9589042300-2302
ORF1ab/nsp2499F499SF679SnonsyntTTtCC7320.02739732300-2302
ORF1ab/nsp2499F499SF679SnonsyntTTtCA7310.01369862300-2302
ORF1ab/nsp2499F499VF679VnonsynTttGtt131312300-2302
ORF1ab/nsp2499F499del1F679del1delTtt-tt12110.9166672300-2302
ORF1ab/nsp2499F499del1F679del1delttTtt-1210.08333332300-2302
ORF1ab/nsp2499F499YF679YnonsyntTttAt980.8888892300-2302
ORF1ab/nsp2499F499YF679YnonsyntTTtAC910.1111112300-2302
ORF1ab/nsp2499F499IF679InonsynTttAtt540.82300-2302
ORF1ab/nsp2499F499IF679InonsynTtTAtC510.22300-2302
ORF1ab/nsp2499F499CF679CnonsyntTttGt4412300-2302
ORF1ab/nsp2499F499PF679PnonsynTTTCCC420.52300-2302
ORF1ab/nsp2499F499PF679PnonsynTTTCCG410.252300-2302
ORF1ab/nsp2499F499PF679PnonsynTTTCCA410.252300-2302
ORF1ab/nsp2499F499TF679TnonsynTTTACC320.6666672300-2302
ORF1ab/nsp2499F499TF679TnonsynTTTACG310.3333332300-2302
ORF1ab/nsp2499F499HF679HnonsynTTTCAC1112300-2302

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/nsp2499F499LTttCtt410463All0.000078
ORF1ab/nsp2499F499LttTttA35463All0.000007
ORF1ab/nsp2499F499LttTttG13463All0.000002
ORF1ab/nsp2499F499LTtTCtG3463All0.000001
ORF1ab/nsp2499F499LTtTCtA2463All0
ORF1ab/nsp2499F499LTttCtt134136B.10.001227
ORF1ab/nsp2499F499LttTttA2136B.10.000018
ORF1ab/nsp2499F499FttTttC112112All0.000021
ORF1ab/nsp2499F499FttTttC7777AY.1180.004824
ORF1ab/nsp2499F499delTTT---7474All0.000014
ORF1ab/nsp2499F499StTttCt7073All0.000013
ORF1ab/nsp2499F499StTTtCC273All0
ORF1ab/nsp2499F499StTTtCA173All0
ORF1ab/nsp2499F499LTttCtt6666AY.46.40.010857
ORF1ab/nsp2499F499LTttCtt5959B.1.5631
ORF1ab/nsp2499F499LttTttA2541B.1.617.20.000094
ORF1ab/nsp2499F499LTttCtt1341B.1.617.20.000049
ORF1ab/nsp2499F499LTtTCtA141B.1.617.20.000004
ORF1ab/nsp2499F499LTtTCtG141B.1.617.20.000004
ORF1ab/nsp2499F499LttTttG141B.1.617.20.000004
ORF1ab/nsp2499F499LTttCtt2323AY.40.000036
ORF1ab/nsp2499F499StTttCt2223B.1.1.70.00002
ORF1ab/nsp2499F499StTTtCC123B.1.1.70.000001
ORF1ab/nsp2499F499LTttCtt2222AY.1020.000583
ORF1ab/nsp2499F499delTTT---2121B.1.1.70.000019
ORF1ab/nsp2499F499VTttGtt1313All0.000002
ORF1ab/nsp2499F499del1Ttt-tt1112All0.000002
ORF1ab/nsp2499F499del1ttTtt-112All0
ORF1ab/nsp2499F499LTttCtt1111AY.30.000109
ORF1ab/nsp2499F499LTttCtt810B.1.20.00007
ORF1ab/nsp2499F499LttTttG210B.1.20.000018
ORF1ab/nsp2499F499YtTttAt89All0.000002
ORF1ab/nsp2499F499YtTTtAC19All0
ORF1ab/nsp2499F499StTttCt99AY.40.000014
ORF1ab/nsp2499F499LTttCtt69AY.440.000037
ORF1ab/nsp2499F499LttTttG39AY.440.000018
ORF1ab/nsp2499F499LTttCtt77AY.98.10.000339
ORF1ab/nsp2499F499FttTttC77B.1.1.70.000006
ORF1ab/nsp2499F499LTttCtt67B.1.1.70.000005
ORF1ab/nsp2499F499LttTttG17B.1.1.70.000001
ORF1ab/nsp2499F499delTTT---660.333333
ORF1ab/nsp2499F499LTttCtt66B.1.3620.009245
ORF1ab/nsp2499F499ITttAtt45All0.000001
ORF1ab/nsp2499F499ITtTAtC15All0
ORF1ab/nsp2499F499YtTttAt55AY.40.000008
ORF1ab/nsp2499F499LTttCtt55AY.430.000022
ORF1ab/nsp2499F499LTttCtt35AY.9.20.00011
ORF1ab/nsp2499F499LTtTCtG25AY.9.20.000073
ORF1ab/nsp2499F499StTttCt55B.10.000046
ORF1ab/nsp2499F499delTTT---55B.10.000046
ORF1ab/nsp2499F499LTttCtt55P.10.000079
ORF1ab/nsp2499F499CtTttGt44All0.000001
ORF1ab/nsp2499F499PTTTCCC24All0
ORF1ab/nsp2499F499PTTTCCG14All0
ORF1ab/nsp2499F499PTTTCCA14All0
ORF1ab/nsp2499F499ITttAtt44AY.250.000024
ORF1ab/nsp2499F499FttTttC44AY.40.000006
ORF1ab/nsp2499F499delTTT---44AY.430.000018
ORF1ab/nsp2499F499StTttCt44AY.430.000018
ORF1ab/nsp2499F499LTttCtt34B.1.10.000054
ORF1ab/nsp2499F499LttTttA14B.1.10.000018
ORF1ab/nsp2499F499StTttCt44B.1.20.000035
ORF1ab/nsp2499F499StTttCt44B.1.5610.001588
ORF1ab/nsp2499F499StTttCt44B.1.5960.000349
ORF1ab/nsp2499F499delTTT---44B.1.617.20.000015
ORF1ab/nsp2499F499TTTTACC23All0
ORF1ab/nsp2499F499TTTTACG13All0
ORF1ab/nsp2499F499LTttCtt33AY.1030.000019
ORF1ab/nsp2499F499PTTTCCG13AY.1130.000142
ORF1ab/nsp2499F499PTTTCCC13AY.1130.000142
ORF1ab/nsp2499F499PTTTCCA13AY.1130.000142
ORF1ab/nsp2499F499VTttGtt33AY.250.000018
ORF1ab/nsp2499F499LTttCtt33AY.260.000085
ORF1ab/nsp2499F499FttTttC33AY.420.000121
ORF1ab/nsp2499F499FttTttC33AY.430.000013
ORF1ab/nsp2499F499del1Ttt-tt33AY.440.000018
ORF1ab/nsp2499F499LTttCtt33AY.750.000168
ORF1ab/nsp2499F499delTTT---33B.1.1.330.001263
ORF1ab/nsp2499F499LttTttA33N.50.0053
ORF1ab/nsp2499F499FttTttC22AY.1200.000074
ORF1ab/nsp2499F499LTttCtt22AY.230.000139
ORF1ab/nsp2499F499FttTttC22AY.290.000032
ORF1ab/nsp2499F499FttTttC22AY.440.000012
ORF1ab/nsp2499F499StTttCt22AY.440.000012
ORF1ab/nsp2499F499StTTtCC12AY.46.60.000072
ORF1ab/nsp2499F499StTTtCA12AY.46.60.000072
ORF1ab/nsp2499F499FttTttC22AY.60.000082
ORF1ab/nsp2499F499StTttCt22AY.60.000082
ORF1ab/nsp2499F499StTttCt22AY.620.000871
ORF1ab/nsp2499F499delTTT---22AY.990.002099
ORF1ab/nsp2499F499delTTT---22B.1.10.000036
ORF1ab/nsp2499F499VTttGtt22B.1.10.000036
ORF1ab/nsp2499F499LTttCtt22B.1.1.2160.001781
ORF1ab/nsp2499F499delTTT---22B.1.1.3480.001592
ORF1ab/nsp2499F499YtTttAt22B.1.20.000018
ORF1ab/nsp2499F499VTttGtt22B.1.20.000018
ORF1ab/nsp2499F499LTttCtt12B.1.258.170.000104
ORF1ab/nsp2499F499LttTttG12B.1.258.170.000104
ORF1ab/nsp2499F499delTTT---22B.1.4240.016129
ORF1ab/nsp2499F499LTttCtt12B.1.4270.00005
ORF1ab/nsp2499F499LttTttA12B.1.4270.00005
ORF1ab/nsp2499F499delTTT---22B.1.4290.000047
ORF1ab/nsp2499F499del1Ttt-tt22B.1.617.20.000008
ORF1ab/nsp2499F499StTttCt22B.1.617.20.000008
ORF1ab/nsp2499F499FttTttC22B.1.617.20.000008
ORF1ab/nsp2499F499LTttCtt22D.20.00015
ORF1ab/nsp2499F499delTTT---22N.60.014184
ORF1ab/nsp2499F499LttTttG11A0.000387
ORF1ab/nsp2499F499LTttCtt11A.2.40.003367
ORF1ab/nsp2499F499LTtTCtA11A.23.10.000704
ORF1ab/nsp2499F499HTTTCAC11All0
ORF1ab/nsp2499F499LttTttA11AY.1000.000046
ORF1ab/nsp2499F499FttTttC11AY.1020.000027
ORF1ab/nsp2499F499StTttCt11AY.1030.000006
ORF1ab/nsp2499F499delTTT---11AY.1080.001103
ORF1ab/nsp2499F499CtTttGt11AY.1100.000113
ORF1ab/nsp2499F499LTttCtt11AY.1200.000037
ORF1ab/nsp2499F499LttTttG11AY.120.10.000321
ORF1ab/nsp2499F499StTttCt11AY.1210.000135
ORF1ab/nsp2499F499StTttCt11AY.200.000039
ORF1ab/nsp2499F499FttTttC11AY.230.00007
ORF1ab/nsp2499F499delTTT---11AY.250.000006
ORF1ab/nsp2499F499LttTttA11AY.250.000006
ORF1ab/nsp2499F499StTttCt11AY.250.000006
ORF1ab/nsp2499F499delTTT---11AY.29.10.000221
ORF1ab/nsp2499F499FttTttC11AY.30.00001
ORF1ab/nsp2499F499HTTTCAC11AY.30.00001
ORF1ab/nsp2499F499VTttGtt11AY.30.00001
ORF1ab/nsp2499F499LTttCtt11AY.320.000532
ORF1ab/nsp2499F499LTttCtt11AY.330.000067
ORF1ab/nsp2499F499LTttCtt11AY.340.000097
ORF1ab/nsp2499F499LTttCtt11AY.34.10.00051
ORF1ab/nsp2499F499VTttGtt11AY.40.000002
ORF1ab/nsp2499F499CtTttGt11AY.40.000002
ORF1ab/nsp2499F499delTTT---11AY.40.000002
ORF1ab/nsp2499F499LTttCtt11AY.420.00004
ORF1ab/nsp2499F499del1Ttt-tt11AY.430.000004
ORF1ab/nsp2499F499delTTT---11AY.440.000006
ORF1ab/nsp2499F499YtTTtAC11AY.440.000006
ORF1ab/nsp2499F499CtTttGt11AY.440.000006
ORF1ab/nsp2499F499LttTttG11AY.460.000104
ORF1ab/nsp2499F499FttTttC11AY.46.60.000072
ORF1ab/nsp2499F499del1Ttt-tt11AY.540.000095
ORF1ab/nsp2499F499delTTT---11AY.670.000464
ORF1ab/nsp2499F499delTTT---11AY.750.000056
ORF1ab/nsp2499F499StTttCt11AY.770.001127
ORF1ab/nsp2499F499delTTT---11AY.840.000437
ORF1ab/nsp2499F499delTTT---11AY.98.10.000048
ORF1ab/nsp2499F499del1ttTtt-11B0.000128
ORF1ab/nsp2499F499TTTTACG11B.10.000009
ORF1ab/nsp2499F499VTttGtt11B.10.000009
ORF1ab/nsp2499F499del1Ttt-tt11B.10.000009
ORF1ab/nsp2499F499del1Ttt-tt11B.1.10.000018
ORF1ab/nsp2499F499FttTttC11B.1.1.1330.008475
ORF1ab/nsp2499F499LTttCtt11B.1.1.1980.001468
ORF1ab/nsp2499F499LTttCtt11B.1.1.390.00051
ORF1ab/nsp2499F499delTTT---11B.1.1.4160.000905
ORF1ab/nsp2499F499StTttCt11B.1.1.5190.00004
ORF1ab/nsp2499F499delTTT---11B.1.1.5230.001563
ORF1ab/nsp2499F499CtTttGt11B.1.1.70.000001
ORF1ab/nsp2499F499del1Ttt-tt11B.1.1.70.000001
ORF1ab/nsp2499F499VTttGtt11B.1.1.70.000001
ORF1ab/nsp2499F499TTTTACC11B.1.1.70.000001
ORF1ab/nsp2499F499LTttCtt11B.1.110.30.000718
ORF1ab/nsp2499F499ITtTAtC11B.1.1600.000031
ORF1ab/nsp2499F499delTTT---11B.1.1770.000013
ORF1ab/nsp2499F499VTttGtt11B.1.1770.000013
ORF1ab/nsp2499F499LttTttG11B.1.177.230.003236
ORF1ab/nsp2499F499LttTttG11B.1.177.430.001477
ORF1ab/nsp2499F499StTttCt11B.1.177.440.000519
ORF1ab/nsp2499F499StTttCt11B.1.177.650.000665
ORF1ab/nsp2499F499LTttCtt11B.1.177.90.001332
ORF1ab/nsp2499F499delTTT---11B.1.1790.003759
ORF1ab/nsp2499F499FttTttC11B.1.2580.000067
ORF1ab/nsp2499F499VTttGtt11B.1.3510.00003
ORF1ab/nsp2499F499StTttCt11B.1.36.180.00042
ORF1ab/nsp2499F499FttTttC11B.1.36.290.000517
ORF1ab/nsp2499F499LTttCtt11B.1.4040.001302
ORF1ab/nsp2499F499delTTT---11B.1.416.10.001563
ORF1ab/nsp2499F499LttTttA11B.1.4290.000024
ORF1ab/nsp2499F499FttTttC11B.1.438.10.000107
ORF1ab/nsp2499F499LTttCtt11B.1.438.10.000107
ORF1ab/nsp2499F499LTttCtt11B.1.5200.021739
ORF1ab/nsp2499F499delTTT---11B.1.5610.000397
ORF1ab/nsp2499F499del1Ttt-tt11B.1.5960.000087
ORF1ab/nsp2499F499TTTTACC11B.1.617.20.000004
ORF1ab/nsp2499F499PTTTCCC11B.1.617.20.000004
ORF1ab/nsp2499F499LTttCtt11B.1.6200.000946
ORF1ab/nsp2499F499delTTT---11B.340.013699
ORF1ab/nsp2499F499delTTT---11B.570.015152
ORF1ab/nsp2499F499LTttCtt11C.230.005814
ORF1ab/nsp2499F499YtTttAt11P.10.000016
ORF1ab/nsp2499F499delTTT---11P.10.000016
ORF1ab/nsp2499F499StTttCt11P.1.150.000232
ORF1ab/nsp2499F499delTTT---11P.20.000187

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.