CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1478

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/nsp31478D1478DD2296DsyngaTgaC2312231217151-7153
ORF1ab/nsp31478D1478delD2296deldelGAT---10910917151-7153
ORF1ab/nsp31478D1478YD2296YnonsynGatTat28260.9285717151-7153
ORF1ab/nsp31478D1478YD2296YnonsynGaTTaC2820.07142867151-7153
ORF1ab/nsp31478D1478ED2296EnonsyngaTgaG26130.57151-7153
ORF1ab/nsp31478D1478ED2296EnonsyngaTgaA26130.57151-7153
ORF1ab/nsp31478D1478VD2296VnonsyngAtgTt1290.757151-7153
ORF1ab/nsp31478D1478VD2296VnonsyngATgTC1210.08333337151-7153
ORF1ab/nsp31478D1478VD2296VnonsyngATgTG1210.08333337151-7153
ORF1ab/nsp31478D1478VD2296VnonsyngATgTA1210.08333337151-7153
ORF1ab/nsp31478D1478ND2296NnonsynGatAat9917151-7153
ORF1ab/nsp31478D1478AD2296AnonsyngAtgCt7717151-7153
ORF1ab/nsp31478D1478GD2296GnonsyngAtgGt7717151-7153
ORF1ab/nsp31478D1478HD2296HnonsynGatCat5517151-7153
ORF1ab/nsp31478D1478del1D2296del1delgaTga-530.67151-7153
ORF1ab/nsp31478D1478del1D2296del1delGAt-Gt510.27151-7153
ORF1ab/nsp31478D1478del1D2296del1delGAT-NN510.27151-7153
ORF1ab/nsp31478D1478XD2296XnonsynGaTTaG2217151-7153
ORF1ab/nsp31478D1478FD2296FnonsynGAtTTt210.57151-7153
ORF1ab/nsp31478D1478FD2296FnonsynGATTTC210.57151-7153
ORF1ab/nsp31478D1478CD2296CnonsynGAtTGt210.57151-7153
ORF1ab/nsp31478D1478CD2296CnonsynGATTGC210.57151-7153
ORF1ab/nsp31478D1478SD2296SnonsynGATAGC210.57151-7153
ORF1ab/nsp31478D1478SD2296SnonsynGAtTCt210.57151-7153
ORF1ab/nsp31478D1478LD2296LnonsynGATTTG1117151-7153
ORF1ab/nsp31478D1478del2D2296del2delGAt--t1117151-7153
ORF1ab/nsp31478D1478QD2296QnonsynGaTCaG1117151-7153

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/nsp31478D1478DgaTgaC23122312All0.000442
ORF1ab/nsp31478D1478DgaTgaC20442044AE.80.999511
ORF1ab/nsp31478D1478delGAT---109109All0.000021
ORF1ab/nsp31478D1478DgaTgaC5656B.1.1.70.00005
ORF1ab/nsp31478D1478DgaTgaC5454B.1.5210.268657
ORF1ab/nsp31478D1478DgaTgaC4444B.1.177.120.006675
ORF1ab/nsp31478D1478DgaTgaC3131AY.40.000048
ORF1ab/nsp31478D1478YGatTat2628All0.000005
ORF1ab/nsp31478D1478YGaTTaC228All0
ORF1ab/nsp31478D1478delGAT---2828B.1.1.70.000025
ORF1ab/nsp31478D1478EgaTgaA1326All0.000002
ORF1ab/nsp31478D1478EgaTgaG1326All0.000002
ORF1ab/nsp31478D1478VgAtgTt912All0.000002
ORF1ab/nsp31478D1478VgATgTA112All0
ORF1ab/nsp31478D1478VgATgTC112All0
ORF1ab/nsp31478D1478VgATgTG112All0
ORF1ab/nsp31478D1478DgaTgaC1111B.1.5380.08871
ORF1ab/nsp31478D1478NGatAat99All0.000002
ORF1ab/nsp31478D1478DgaTgaC99B.1.10.000163
ORF1ab/nsp31478D1478EgaTgaA79B.1.1.70.000006
ORF1ab/nsp31478D1478EgaTgaG29B.1.1.70.000002
ORF1ab/nsp31478D1478DgaTgaC88B.10.000073
ORF1ab/nsp31478D1478delGAT---88B.1.1770.000105
ORF1ab/nsp31478D1478GgAtgGt77All0.000001
ORF1ab/nsp31478D1478AgAtgCt77All0.000001
ORF1ab/nsp31478D1478delGAT---77B.10.000064
ORF1ab/nsp31478D1478HGatCat55All0.000001
ORF1ab/nsp31478D1478del1gaTga-35All0.000001
ORF1ab/nsp31478D1478del1GAT-NN15All0
ORF1ab/nsp31478D1478del1GAt-Gt15All0
ORF1ab/nsp31478D1478DgaTgaC55B.1.617.20.000019
ORF1ab/nsp31478D1478delGAT---440.222222
ORF1ab/nsp31478D1478delGAT---44AY.40.000006
ORF1ab/nsp31478D1478YGatTat44B.10.000037
ORF1ab/nsp31478D1478delGAT---44B.1.1.2180.030769
ORF1ab/nsp31478D1478DgaTgaC44B.1.1.3110.001433
ORF1ab/nsp31478D1478YGatTat230.111111
ORF1ab/nsp31478D1478YGaTTaC130.055556
ORF1ab/nsp31478D1478VgATgTG130.055556
ORF1ab/nsp31478D1478VgAtgTt130.055556
ORF1ab/nsp31478D1478VgATgTC130.055556
ORF1ab/nsp31478D1478DgaTgaC33AY.290.000047
ORF1ab/nsp31478D1478NGatAat33AY.40.000005
ORF1ab/nsp31478D1478delGAT---33B.1.10.000054
ORF1ab/nsp31478D1478DgaTgaC33B.1.1770.00004
ORF1ab/nsp31478D1478delGAT---33B.1.617.20.000011
ORF1ab/nsp31478D1478XGaTTaG220.111111
ORF1ab/nsp31478D1478EgaTgaG220.111111
ORF1ab/nsp31478D1478FGATTTC120.055556
ORF1ab/nsp31478D1478FGAtTTt120.055556
ORF1ab/nsp31478D1478XGaTTaG22All0
ORF1ab/nsp31478D1478SGAtTCt12All0
ORF1ab/nsp31478D1478SGATAGC12All0
ORF1ab/nsp31478D1478CGATTGC12All0
ORF1ab/nsp31478D1478CGAtTGt12All0
ORF1ab/nsp31478D1478FGAtTTt12All0
ORF1ab/nsp31478D1478FGATTTC12All0
ORF1ab/nsp31478D1478DgaTgaC22AY.1020.000053
ORF1ab/nsp31478D1478DgaTgaC22AY.1030.000012
ORF1ab/nsp31478D1478EgaTgaA22AY.260.000057
ORF1ab/nsp31478D1478YGatTat22AY.40.000003
ORF1ab/nsp31478D1478delGAT---22AY.4.50.000215
ORF1ab/nsp31478D1478EgaTgaG22AY.430.000009
ORF1ab/nsp31478D1478delGAT---22AY.430.000009
ORF1ab/nsp31478D1478DgaTgaC22AY.430.000009
ORF1ab/nsp31478D1478DgaTgaC22AY.440.000012
ORF1ab/nsp31478D1478EgaTgaG22AY.450.000243
ORF1ab/nsp31478D1478EgaTgaG22AY.470.000062
ORF1ab/nsp31478D1478NGatAat22AY.50.000041
ORF1ab/nsp31478D1478AgAtgCt22B.10.000018
ORF1ab/nsp31478D1478VgAtgTt22B.10.000018
ORF1ab/nsp31478D1478DgaTgaC22B.1.1.2310.006192
ORF1ab/nsp31478D1478DgaTgaC22B.1.1.2690.002706
ORF1ab/nsp31478D1478CGATTGC12B.1.1.280.000311
ORF1ab/nsp31478D1478CGAtTGt12B.1.1.280.000311
ORF1ab/nsp31478D1478YGatTat12B.1.1.280.000311
ORF1ab/nsp31478D1478YGaTTaC12B.1.1.280.000311
ORF1ab/nsp31478D1478YGatTat22B.1.1.70.000002
ORF1ab/nsp31478D1478GgAtgGt22B.1.1.70.000002
ORF1ab/nsp31478D1478NGatAat22B.1.1.70.000002
ORF1ab/nsp31478D1478VgAtgTt22B.1.1.70.000002
ORF1ab/nsp31478D1478DgaTgaC22B.1.1600.000062
ORF1ab/nsp31478D1478delGAT---22B.1.177.620.002384
ORF1ab/nsp31478D1478DgaTgaC22B.1.3510.000059
ORF1ab/nsp31478D1478delGAT---22B.1.4110.007407
ORF1ab/nsp31478D1478YGatTat22B.1.466.20.000782
ORF1ab/nsp31478D1478YGatTat22B.1.5960.000174
ORF1ab/nsp31478D1478delGAT---22B.1.5960.000174
ORF1ab/nsp31478D1478delGAT---22C.350.001548
ORF1ab/nsp31478D1478VgATgTA12P.1.10.000318
ORF1ab/nsp31478D1478VgAtgTt12P.1.10.000318
ORF1ab/nsp31478D1478HGatCat110.055556
ORF1ab/nsp31478D1478DgaTgaC110.055556
ORF1ab/nsp31478D1478GgAtgGt110.055556
ORF1ab/nsp31478D1478QGaTCaG110.055556
ORF1ab/nsp31478D1478LGATTTG110.055556
ORF1ab/nsp31478D1478VgAtgTt11A.50.001923
ORF1ab/nsp31478D1478delGAT---11AD.20.000219
ORF1ab/nsp31478D1478QGaTCaG11All0
ORF1ab/nsp31478D1478del2GAt--t11All0
ORF1ab/nsp31478D1478LGATTTG11All0
ORF1ab/nsp31478D1478delGAT---11AY.1010.00049
ORF1ab/nsp31478D1478delGAT---11AY.1030.000006
ORF1ab/nsp31478D1478EgaTgaG11AY.1030.000006
ORF1ab/nsp31478D1478delGAT---11AY.1080.001103
ORF1ab/nsp31478D1478HGatCat11AY.1170.000085
ORF1ab/nsp31478D1478YGatTat11AY.1180.000063
ORF1ab/nsp31478D1478delGAT---11AY.1190.000035
ORF1ab/nsp31478D1478DgaTgaC11AY.1190.000035
ORF1ab/nsp31478D1478delGAT---11AY.1200.000037
ORF1ab/nsp31478D1478del1gaTga-11AY.120.10.000321
ORF1ab/nsp31478D1478DgaTgaC11AY.190.00114
ORF1ab/nsp31478D1478YGatTat11AY.240.000431
ORF1ab/nsp31478D1478HGatCat11AY.250.000006
ORF1ab/nsp31478D1478DgaTgaC11AY.250.000006
ORF1ab/nsp31478D1478delGAT---11AY.250.000006
ORF1ab/nsp31478D1478GgAtgGt11AY.250.000006
ORF1ab/nsp31478D1478YGatTat11AY.250.000006
ORF1ab/nsp31478D1478delGAT---11AY.30.00001
ORF1ab/nsp31478D1478delGAT---11AY.360.000148
ORF1ab/nsp31478D1478YGatTat11AY.370.000316
ORF1ab/nsp31478D1478AgAtgCt11AY.39.10.00004
ORF1ab/nsp31478D1478DgaTgaC11AY.4.20.000022
ORF1ab/nsp31478D1478delGAT---11AY.4.30.000842
ORF1ab/nsp31478D1478SGAtTCt11AY.430.000004
ORF1ab/nsp31478D1478del1GAt-Gt11AY.440.000006
ORF1ab/nsp31478D1478DgaTgaC11AY.470.000031
ORF1ab/nsp31478D1478DgaTgaC11AY.50.000021
ORF1ab/nsp31478D1478DgaTgaC11AY.5.10.003759
ORF1ab/nsp31478D1478delGAT---11AY.590.00053
ORF1ab/nsp31478D1478delGAT---11AY.600.000938
ORF1ab/nsp31478D1478delGAT---11AY.660.00107
ORF1ab/nsp31478D1478delGAT---11AY.670.000464
ORF1ab/nsp31478D1478DgaTgaC11AY.740.000116
ORF1ab/nsp31478D1478delGAT---11AY.840.000437
ORF1ab/nsp31478D1478DgaTgaC11AY.880.000884
ORF1ab/nsp31478D1478delGAT---11AY.90.000068
ORF1ab/nsp31478D1478YGatTat11AY.90.000068
ORF1ab/nsp31478D1478DgaTgaC11AY.960.002075
ORF1ab/nsp31478D1478delGAT---11AY.990.001049
ORF1ab/nsp31478D1478DgaTgaC11B0.000128
ORF1ab/nsp31478D1478GgAtgGt11B.10.000009
ORF1ab/nsp31478D1478EgaTgaA11B.10.000009
ORF1ab/nsp31478D1478AgAtgCt11B.1.1.3180.000302
ORF1ab/nsp31478D1478delGAT---11B.1.1.370.000193
ORF1ab/nsp31478D1478VgAtgTt11B.1.1.3710.010417
ORF1ab/nsp31478D1478NGatAat11B.1.1.4110.014706
ORF1ab/nsp31478D1478delGAT---11B.1.1.460.004367
ORF1ab/nsp31478D1478delGAT---11B.1.1.4640.001473
ORF1ab/nsp31478D1478delGAT---11B.1.1.5250.005464
ORF1ab/nsp31478D1478del1GAT-NN11B.1.1.70.000001
ORF1ab/nsp31478D1478del2GAt--t11B.1.1.70.000001
ORF1ab/nsp31478D1478AgAtgCt11B.1.1.70.000001
ORF1ab/nsp31478D1478delGAT---11B.1.1.700.000341
ORF1ab/nsp31478D1478DgaTgaC11B.1.1280.000635
ORF1ab/nsp31478D1478DgaTgaC11B.1.160.140.002119
ORF1ab/nsp31478D1478YGatTat11B.1.1770.000013
ORF1ab/nsp31478D1478YGatTat11B.1.177.50.001242
ORF1ab/nsp31478D1478delGAT---11B.1.177.530.002392
ORF1ab/nsp31478D1478delGAT---11B.1.177.60.000977
ORF1ab/nsp31478D1478DgaTgaC11B.1.177.730.000566
ORF1ab/nsp31478D1478YGatTat11B.1.177.770.000726
ORF1ab/nsp31478D1478delGAT---11B.1.177.90.001332
ORF1ab/nsp31478D1478delGAT---11B.1.20.000009
ORF1ab/nsp31478D1478YGatTat11B.1.20.000009
ORF1ab/nsp31478D1478NGatAat11B.1.20.000009
ORF1ab/nsp31478D1478EgaTgaA11B.1.20.000009
ORF1ab/nsp31478D1478del1gaTga-11B.1.20.000009
ORF1ab/nsp31478D1478AgAtgCt11B.1.20.000009
ORF1ab/nsp31478D1478delGAT---11B.1.2210.000071
ORF1ab/nsp31478D1478GgAtgGt11B.1.2220.001692
ORF1ab/nsp31478D1478delGAT---11B.1.2580.000067
ORF1ab/nsp31478D1478DgaTgaC11B.1.2580.000067
ORF1ab/nsp31478D1478delGAT---11B.1.2650.001271
ORF1ab/nsp31478D1478DgaTgaC11B.1.2790.000514
ORF1ab/nsp31478D1478del1gaTga-11B.1.360.000146
ORF1ab/nsp31478D1478DgaTgaC11B.1.36.100.004785
ORF1ab/nsp31478D1478DgaTgaC11B.1.3670.000792
ORF1ab/nsp31478D1478delGAT---11B.1.416.10.001563
ORF1ab/nsp31478D1478YGatTat11B.1.4270.00005
ORF1ab/nsp31478D1478GgAtgGt11B.1.4270.00005
ORF1ab/nsp31478D1478YGatTat11B.1.4290.000024
ORF1ab/nsp31478D1478DgaTgaC11B.1.4290.000024
ORF1ab/nsp31478D1478delGAT---11B.1.5260.000024
ORF1ab/nsp31478D1478delGAT---11B.1.5330.009615
ORF1ab/nsp31478D1478delGAT---11B.1.5770.000687
ORF1ab/nsp31478D1478EgaTgaG11B.1.617.10.000129
ORF1ab/nsp31478D1478VgAtgTt11B.1.617.20.000004
ORF1ab/nsp31478D1478SGATAGC11B.1.617.20.000004
ORF1ab/nsp31478D1478EgaTgaG11B.1.617.20.000004
ORF1ab/nsp31478D1478AgAtgCt11B.1.619.10.000641
ORF1ab/nsp31478D1478DgaTgaC11B.1.619.10.000641
ORF1ab/nsp31478D1478delGAT---11B.1.6210.000089
ORF1ab/nsp31478D1478EgaTgaA11D.20.000075
ORF1ab/nsp31478D1478HGatCat11D.20.000075
ORF1ab/nsp31478D1478HGatCat11P.10.000016
ORF1ab/nsp31478D1478delGAT---11P.10.000016
ORF1ab/nsp31478D1478DgaTgaC11P.10.000016
ORF1ab/nsp31478D1478EgaTgaA11P.1.10.000318
ORF1ab/nsp31478D1478delGAT---11P.1.150.000232
ORF1ab/nsp31478D1478DgaTgaC11P.20.000187
ORF1ab/nsp31478D1478DgaTgaC11Q.80.000165

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.