CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1569

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/nsp31569F1569VF2387VnonsynTttGtt9007900717424-7426
ORF1ab/nsp31569F1569LF2387LnonsynttTttA2281150.5043867424-7426
ORF1ab/nsp31569F1569LF2387LnonsynTttCtt228950.4166677424-7426
ORF1ab/nsp31569F1569LF2387LnonsynttTttG228180.07894747424-7426
ORF1ab/nsp31569F1569FF2387FsynttTttC646417424-7426
ORF1ab/nsp31569F1569delF2387deldelTTT---575717424-7426
ORF1ab/nsp31569F1569CF2387CnonsyntTttGt343417424-7426
ORF1ab/nsp31569F1569IF2387InonsynTttAtt161617424-7426
ORF1ab/nsp31569F1569SF2387SnonsyntTttCt16150.93757424-7426
ORF1ab/nsp31569F1569SF2387SnonsynTTtAGt1610.06257424-7426
ORF1ab/nsp31569F1569del1F2387del1delTtt-tt11100.9090917424-7426
ORF1ab/nsp31569F1569del1F2387del1delTtT-tG1110.09090917424-7426
ORF1ab/nsp31569F1569YF2387YnonsyntTttAt101017424-7426
ORF1ab/nsp31569F1569del2F2387del2delTTt--t430.757424-7426
ORF1ab/nsp31569F1569del2F2387del2deltTTt--410.257424-7426
ORF1ab/nsp31569F1569HF2387HnonsynTTtCAt1117424-7426
ORF1ab/nsp31569F1569XF2387XnonsyntTTtAA1117424-7426

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/nsp31569F1569VTttGtt90079007All0.001723
ORF1ab/nsp31569F1569VTttGtt85408540C.370.991179
ORF1ab/nsp31569F1569VTttGtt371371C.37.10.971204
ORF1ab/nsp31569F1569LttTttA115228All0.000022
ORF1ab/nsp31569F1569LTttCtt95228All0.000018
ORF1ab/nsp31569F1569LttTttG18228All0.000003
ORF1ab/nsp31569F1569FttTttC6464All0.000012
ORF1ab/nsp31569F1569LttTttA6062AY.40.000093
ORF1ab/nsp31569F1569LttTttG262AY.40.000003
ORF1ab/nsp31569F1569delTTT---5757All0.000011
ORF1ab/nsp31569F1569LTttCtt1836B.1.1.70.000016
ORF1ab/nsp31569F1569LttTttA1236B.1.1.70.000011
ORF1ab/nsp31569F1569LttTttG636B.1.1.70.000005
ORF1ab/nsp31569F1569CtTttGt3434All0.000007
ORF1ab/nsp31569F1569delTTT---2121B.1.1.70.000019
ORF1ab/nsp31569F1569FttTttC2020AY.40.000031
ORF1ab/nsp31569F1569LttTttA2020B.1.1.2840.002148
ORF1ab/nsp31569F1569LTttCtt1818AY.250.000108
ORF1ab/nsp31569F1569CtTttGt1717B.1.1.70.000015
ORF1ab/nsp31569F1569ITttAtt1616All0.000003
ORF1ab/nsp31569F1569StTttCt1516All0.000003
ORF1ab/nsp31569F1569STTtAGt116All0
ORF1ab/nsp31569F1569LTttCtt1616B.1.258.170.001664
ORF1ab/nsp31569F1569VTttGtt1414B.1.10.000254
ORF1ab/nsp31569F1569CtTttGt1212B.1.3810.09375
ORF1ab/nsp31569F1569del1Ttt-tt1011All0.000002
ORF1ab/nsp31569F1569del1TtT-tG111All0
ORF1ab/nsp31569F1569ITttAtt1111B.1.1600.000343
ORF1ab/nsp31569F1569YtTttAt1010All0.000002
ORF1ab/nsp31569F1569FttTttC1010B.1.351.20.003026
ORF1ab/nsp31569F1569VTttGtt99B.10.000082
ORF1ab/nsp31569F1569VTttGtt88B.1.617.20.00003
ORF1ab/nsp31569F1569LTttCtt77AY.9.10.000586
ORF1ab/nsp31569F1569LTttCtt57B.10.000046
ORF1ab/nsp31569F1569LttTttA17B.10.000009
ORF1ab/nsp31569F1569LttTttG17B.10.000009
ORF1ab/nsp31569F1569VTttGtt77P.1.150.001626
ORF1ab/nsp31569F1569LttTttA66AY.160.002278
ORF1ab/nsp31569F1569delTTT---66B.10.000055
ORF1ab/nsp31569F1569FttTttC55B.10.000046
ORF1ab/nsp31569F1569LttTttG55B.1.1600.000156
ORF1ab/nsp31569F1569VTttGtt55P.10.000079
ORF1ab/nsp31569F1569del2TTt--t34All0.000001
ORF1ab/nsp31569F1569del2tTTt--14All0
ORF1ab/nsp31569F1569FttTttC44AY.260.000113
ORF1ab/nsp31569F1569VTttGtt44AY.40.000006
ORF1ab/nsp31569F1569VTttGtt44B.1.1.3720.002755
ORF1ab/nsp31569F1569StTttCt44B.1.1.70.000004
ORF1ab/nsp31569F1569LTttCtt44P.10.000063
ORF1ab/nsp31569F1569FttTttC33AY.200.000117
ORF1ab/nsp31569F1569delTTT---33AY.40.000005
ORF1ab/nsp31569F1569LttTttA13AY.430.000004
ORF1ab/nsp31569F1569LttTttG13AY.430.000004
ORF1ab/nsp31569F1569LTttCtt13AY.430.000004
ORF1ab/nsp31569F1569del1Ttt-tt33AY.440.000018
ORF1ab/nsp31569F1569LTttCtt23AY.440.000012
ORF1ab/nsp31569F1569LttTttG13AY.440.000006
ORF1ab/nsp31569F1569VTttGtt33AY.470.000093
ORF1ab/nsp31569F1569LTttCtt33AY.540.000286
ORF1ab/nsp31569F1569StTttCt23B.10.000018
ORF1ab/nsp31569F1569STTtAGt13B.10.000009
ORF1ab/nsp31569F1569VTttGtt33B.1.1.5280.014423
ORF1ab/nsp31569F1569LttTttA23B.1.20.000018
ORF1ab/nsp31569F1569LTttCtt13B.1.20.000009
ORF1ab/nsp31569F1569VTttGtt33B.1.5260.000071
ORF1ab/nsp31569F1569FttTttC33B.1.617.20.000011
ORF1ab/nsp31569F1569LTttCtt23B.1.617.20.000008
ORF1ab/nsp31569F1569LttTttA13B.1.617.20.000004
ORF1ab/nsp31569F1569LttTttA220.111111
ORF1ab/nsp31569F1569FttTttC22AY.1030.000012
ORF1ab/nsp31569F1569YtTttAt22AY.250.000012
ORF1ab/nsp31569F1569delTTT---22AY.250.000012
ORF1ab/nsp31569F1569LttTttA22AY.260.000057
ORF1ab/nsp31569F1569LTttCtt22AY.290.000032
ORF1ab/nsp31569F1569delTTT---22AY.350.000466
ORF1ab/nsp31569F1569YtTttAt22AY.360.000296
ORF1ab/nsp31569F1569FttTttC22AY.390.000049
ORF1ab/nsp31569F1569VTttGtt22AY.4.20.000043
ORF1ab/nsp31569F1569FttTttC22AY.430.000009
ORF1ab/nsp31569F1569del1Ttt-tt22B.10.000018
ORF1ab/nsp31569F1569LTttCtt22B.1.10.000036
ORF1ab/nsp31569F1569VTttGtt22B.1.1.280.000622
ORF1ab/nsp31569F1569VTttGtt22B.1.1.3040.005618
ORF1ab/nsp31569F1569YtTttAt22B.1.1.3060.000877
ORF1ab/nsp31569F1569YtTttAt22B.1.1.70.000002
ORF1ab/nsp31569F1569VTttGtt22B.1.1.70.000002
ORF1ab/nsp31569F1569LTttCtt12B.1.1770.000013
ORF1ab/nsp31569F1569LttTttA12B.1.1770.000013
ORF1ab/nsp31569F1569VTttGtt22B.1.20.000018
ORF1ab/nsp31569F1569LttTttA22B.1.3510.000059
ORF1ab/nsp31569F1569ITttAtt22B.1.351.20.000605
ORF1ab/nsp31569F1569VTttGtt22B.1.466.20.000782
ORF1ab/nsp31569F1569VTttGtt22C.350.001548
ORF1ab/nsp31569F1569VTttGtt22C.390.037736
ORF1ab/nsp31569F1569VTttGtt22P.1.10.000635
ORF1ab/nsp31569F1569VTttGtt22P.1.120.000968
ORF1ab/nsp31569F1569delTTT---11A0.000387
ORF1ab/nsp31569F1569LttTttG11A.10.000282
ORF1ab/nsp31569F1569LTttCtt11AD.20.000219
ORF1ab/nsp31569F1569XtTTtAA11All0
ORF1ab/nsp31569F1569HTTtCAt11All0
ORF1ab/nsp31569F1569del1Ttt-tt11AY.1000.000046
ORF1ab/nsp31569F1569LttTttG11AY.1030.000006
ORF1ab/nsp31569F1569LTttCtt11AY.1130.000142
ORF1ab/nsp31569F1569FttTttC11AY.1160.000287
ORF1ab/nsp31569F1569StTttCt11AY.1180.000063
ORF1ab/nsp31569F1569VTttGtt11AY.1190.000035
ORF1ab/nsp31569F1569StTttCt11AY.1200.000037
ORF1ab/nsp31569F1569VTttGtt11AY.1200.000037
ORF1ab/nsp31569F1569LTttCtt11AY.16.10.00047
ORF1ab/nsp31569F1569LttTttA11AY.200.000039
ORF1ab/nsp31569F1569LttTttA11AY.240.000431
ORF1ab/nsp31569F1569delTTT---11AY.240.000431
ORF1ab/nsp31569F1569StTttCt11AY.250.000006
ORF1ab/nsp31569F1569del1TtT-tG11AY.250.000006
ORF1ab/nsp31569F1569VTttGtt11AY.250.000006
ORF1ab/nsp31569F1569LTttCtt11AY.30.00001
ORF1ab/nsp31569F1569FttTttC11AY.3.10.000085
ORF1ab/nsp31569F1569del2tTTt--11AY.320.000532
ORF1ab/nsp31569F1569VTttGtt11AY.330.000067
ORF1ab/nsp31569F1569LTttCtt11AY.39.10.00004
ORF1ab/nsp31569F1569FttTttC11AY.39.10.00004
ORF1ab/nsp31569F1569ITttAtt11AY.40.000002
ORF1ab/nsp31569F1569CtTttGt11AY.40.000002
ORF1ab/nsp31569F1569StTttCt11AY.40.000002
ORF1ab/nsp31569F1569FttTttC11AY.420.00004
ORF1ab/nsp31569F1569delTTT---11AY.430.000004
ORF1ab/nsp31569F1569FttTttC11AY.440.000006
ORF1ab/nsp31569F1569delTTT---11AY.460.000104
ORF1ab/nsp31569F1569LTttCtt11AY.46.40.000165
ORF1ab/nsp31569F1569VTttGtt11AY.46.60.000072
ORF1ab/nsp31569F1569YtTttAt11AY.470.000031
ORF1ab/nsp31569F1569VTttGtt11AY.50.000021
ORF1ab/nsp31569F1569LTttCtt11AY.50.000021
ORF1ab/nsp31569F1569delTTT---11AY.660.00107
ORF1ab/nsp31569F1569del1Ttt-tt11AY.710.000475
ORF1ab/nsp31569F1569delTTT---11AY.750.000056
ORF1ab/nsp31569F1569LttTttA11AY.750.000056
ORF1ab/nsp31569F1569delTTT---11AY.75.10.00018
ORF1ab/nsp31569F1569VTttGtt11AY.75.10.00018
ORF1ab/nsp31569F1569LttTttA11AY.780.001541
ORF1ab/nsp31569F1569del2TTt--t11AY.90.000068
ORF1ab/nsp31569F1569FttTttC11AY.98.10.000048
ORF1ab/nsp31569F1569delTTT---11AY.99.10.001553
ORF1ab/nsp31569F1569ITttAtt11B.10.000009
ORF1ab/nsp31569F1569CtTttGt11B.10.000009
ORF1ab/nsp31569F1569delTTT---11B.1.10.000018
ORF1ab/nsp31569F1569XtTTtAA11B.1.10.000018
ORF1ab/nsp31569F1569VTttGtt11B.1.1.10.000327
ORF1ab/nsp31569F1569FttTttC11B.1.1.2280.003049
ORF1ab/nsp31569F1569LTttCtt11B.1.1.2750.011236
ORF1ab/nsp31569F1569FttTttC11B.1.1.280.000311
ORF1ab/nsp31569F1569delTTT---11B.1.1.3110.000358
ORF1ab/nsp31569F1569delTTT---11B.1.1.3150.008475
ORF1ab/nsp31569F1569LttTttA11B.1.1.3170.000412
ORF1ab/nsp31569F1569VTttGtt11B.1.1.3480.000796
ORF1ab/nsp31569F1569FttTttC11B.1.1.3540.004386
ORF1ab/nsp31569F1569VTttGtt11B.1.1.4090.002833
ORF1ab/nsp31569F1569delTTT---11B.1.1.4480.002033
ORF1ab/nsp31569F1569delTTT---11B.1.1.460.004367
ORF1ab/nsp31569F1569FttTttC11B.1.1.630.000386
ORF1ab/nsp31569F1569FttTttC11B.1.1.70.000001
ORF1ab/nsp31569F1569del1Ttt-tt11B.1.1.70.000001
ORF1ab/nsp31569F1569del2TTt--t11B.1.1.70.000001
ORF1ab/nsp31569F1569HTTtCAt11B.1.1.70.000001
ORF1ab/nsp31569F1569ITttAtt11B.1.1.70.000001
ORF1ab/nsp31569F1569delTTT---11B.1.1400.018868
ORF1ab/nsp31569F1569delTTT---11B.1.1610.017241
ORF1ab/nsp31569F1569delTTT---11B.1.1770.000013
ORF1ab/nsp31569F1569delTTT---11B.1.177.510.004566
ORF1ab/nsp31569F1569StTttCt11B.1.177.870.000728
ORF1ab/nsp31569F1569delTTT---11B.1.20.000009
ORF1ab/nsp31569F1569StTttCt11B.1.20.000009
ORF1ab/nsp31569F1569del1Ttt-tt11B.1.20.000009
ORF1ab/nsp31569F1569YtTttAt11B.1.2100.002132
ORF1ab/nsp31569F1569VTttGtt11B.1.2210.000071
ORF1ab/nsp31569F1569VTttGtt11B.1.2220.001692
ORF1ab/nsp31569F1569delTTT---11B.1.230.006061
ORF1ab/nsp31569F1569delTTT---11B.1.2580.000067
ORF1ab/nsp31569F1569StTttCt11B.1.3110.000275
ORF1ab/nsp31569F1569del2TTt--t11B.1.3510.00003
ORF1ab/nsp31569F1569CtTttGt11B.1.3510.00003
ORF1ab/nsp31569F1569LTttCtt11B.1.438.10.000107
ORF1ab/nsp31569F1569delTTT---11B.1.5610.000397
ORF1ab/nsp31569F1569del1Ttt-tt11B.1.5760.000907
ORF1ab/nsp31569F1569FttTttC11B.1.5950.000261
ORF1ab/nsp31569F1569VTttGtt11B.1.5960.000087
ORF1ab/nsp31569F1569LTttCtt11B.1.617.10.000129
ORF1ab/nsp31569F1569CtTttGt11B.1.617.20.000004
ORF1ab/nsp31569F1569delTTT---11B.1.617.20.000004
ORF1ab/nsp31569F1569delTTT---11B.1.6210.000089
ORF1ab/nsp31569F1569StTttCt11B.1.6370.000073
ORF1ab/nsp31569F1569LTttCtt11B.3.10.001658
ORF1ab/nsp31569F1569LTttCtt11C.300.001727
ORF1ab/nsp31569F1569VTttGtt11C.36.3.10.002717
ORF1ab/nsp31569F1569VTttGtt11C.400.027778
ORF1ab/nsp31569F1569StTttCt11D.20.000075
ORF1ab/nsp31569F1569LTttCtt11D.20.000075
ORF1ab/nsp31569F1569FttTttC11P.1.100.000269
ORF1ab/nsp31569F1569VTttGtt11P.1.170.000162
ORF1ab/nsp31569F1569CtTttGt11Q.40.000455

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.