CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp1 : CodonNum = 128

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/nsp1128N128NN128NsynaaTaaC2882881647-649
ORF1ab/nsp1128N128DN128DnonsynAatGat1181181647-649
ORF1ab/nsp1128N128SN128SnonsynaAtaGt95951647-649
ORF1ab/nsp1128N128delN128deldelAAT---48481647-649
ORF1ab/nsp1128N128TN128TnonsynaAtaCt27271647-649
ORF1ab/nsp1128N128YN128YnonsynAatTat18181647-649
ORF1ab/nsp1128N128IN128InonsynaAtaTt13131647-649
ORF1ab/nsp1128N128KN128KnonsynaaTaaA11100.909091647-649
ORF1ab/nsp1128N128KN128KnonsynaaTaaG1110.0909091647-649
ORF1ab/nsp1128N128HN128HnonsynAatCat10101647-649
ORF1ab/nsp1128N128del1N128del1delaaTaa-1040.4647-649
ORF1ab/nsp1128N128del1N128del1delAaT-aN1040.4647-649
ORF1ab/nsp1128N128del1N128del1delAat-at1020.2647-649
ORF1ab/nsp1128N128del2N128del2delaATa--441647-649
ORF1ab/nsp1128N128GN128GnonsynAAtGGt331647-649
ORF1ab/nsp1128N128LN128LnonsynAATCTG221647-649
ORF1ab/nsp1128N128XN128XnonsynAaTTaA221647-649
ORF1ab/nsp1128N128EN128EnonsynAaTGaA221647-649
ORF1ab/nsp1128N128VN128VnonsynAAtGTt221647-649
ORF1ab/nsp1128N128QN128QnonsynAaTCaA111647-649

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/nsp1128N128NaaTaaC288288All0.000055
ORF1ab/nsp1128N128DAatGat118118All0.000023
ORF1ab/nsp1128N128SaAtaGt9595All0.000018
ORF1ab/nsp1128N128NaaTaaC6363AY.40.000098
ORF1ab/nsp1128N128DAatGat5656AY.40.000087
ORF1ab/nsp1128N128delAAT---4848All0.000009
ORF1ab/nsp1128N128NaaTaaC3232B.1.1.70.000029
ORF1ab/nsp1128N128TaAtaCt2727All0.000005
ORF1ab/nsp1128N128SaAtaGt2323AY.1030.000143
ORF1ab/nsp1128N128NaaTaaC1919B.1.20.000167
ORF1ab/nsp1128N128YAatTat1818All0.000003
ORF1ab/nsp1128N128NaaTaaC1414AY.390.000346
ORF1ab/nsp1128N128SaAtaGt1414B.1.1770.000184
ORF1ab/nsp1128N128IaAtaTt1313All0.000002
ORF1ab/nsp1128N128TaAtaCt1212AY.40.000019
ORF1ab/nsp1128N128DAatGat1212AY.440.000073
ORF1ab/nsp1128N128SaAtaGt1212B.1.1.70.000011
ORF1ab/nsp1128N128KaaTaaA1011All0.000002
ORF1ab/nsp1128N128KaaTaaG111All0
ORF1ab/nsp1128N128DAatGat1111B.10.000101
ORF1ab/nsp1128N128NaaTaaC1111B.1.1.2220.002244
ORF1ab/nsp1128N128NaaTaaC1111B.1.1770.000145
ORF1ab/nsp1128N128HAatCat1010All0.000002
ORF1ab/nsp1128N128del1AaT-aN410All0.000001
ORF1ab/nsp1128N128del1aaTaa-410All0.000001
ORF1ab/nsp1128N128del1Aat-at210All0
ORF1ab/nsp1128N128SaAtaGt1010AY.40.000016
ORF1ab/nsp1128N128NaaTaaC99B.1.10.000163
ORF1ab/nsp1128N128NaaTaaC99B.1.4270.000454
ORF1ab/nsp1128N128SaAtaGt99B.1.617.20.000034
ORF1ab/nsp1128N128NaaTaaC99B.1.617.20.000034
ORF1ab/nsp1128N128NaaTaaC88AY.230.000558
ORF1ab/nsp1128N128NaaTaaC77AY.30.00007
ORF1ab/nsp1128N128NaaTaaC77AY.430.000031
ORF1ab/nsp1128N128NaaTaaC77AY.440.000043
ORF1ab/nsp1128N128delAAT---77B.1.1.70.000006
ORF1ab/nsp1128N128NaaTaaC66AY.98.10.000291
ORF1ab/nsp1128N128TaAtaCt66AY.99.20.000553
ORF1ab/nsp1128N128NaaTaaC55A.300.714286
ORF1ab/nsp1128N128SaAtaGt55AY.470.000156
ORF1ab/nsp1128N128NaaTaaC55B.10.000046
ORF1ab/nsp1128N128NaaTaaC44AD.20.000876
ORF1ab/nsp1128N128del2aATa--44All0.000001
ORF1ab/nsp1128N128NaaTaaC44AY.1130.00057
ORF1ab/nsp1128N128YAatTat44AY.40.000006
ORF1ab/nsp1128N128delAAT---44B.1.1.330.001684
ORF1ab/nsp1128N128delAAT---44B.1.1.3480.003185
ORF1ab/nsp1128N128NaaTaaC44B.1.6210.000354
ORF1ab/nsp1128N128KaaTaaA330.166667
ORF1ab/nsp1128N128GAAtGGt33All0.000001
ORF1ab/nsp1128N128NaaTaaC33AY.1030.000019
ORF1ab/nsp1128N128NaaTaaC33AY.260.000085
ORF1ab/nsp1128N128DAatGat33AY.30.00003
ORF1ab/nsp1128N128IaAtaTt33AY.40.000005
ORF1ab/nsp1128N128DAatGat33AY.430.000013
ORF1ab/nsp1128N128NaaTaaC33AY.650.001599
ORF1ab/nsp1128N128SaAtaGt33B.10.000027
ORF1ab/nsp1128N128SaAtaGt33B.1.10.000054
ORF1ab/nsp1128N128NaaTaaC33B.1.1.3170.001235
ORF1ab/nsp1128N128NaaTaaC33B.1.1600.000094
ORF1ab/nsp1128N128DAatGat33B.1.3560.005181
ORF1ab/nsp1128N128HAatCat33B.1.5960.000261
ORF1ab/nsp1128N128DAatGat33B.1.617.20.000011
ORF1ab/nsp1128N128DAatGat220.111111
ORF1ab/nsp1128N128EAaTGaA220.111111
ORF1ab/nsp1128N128LAATCTG22All0
ORF1ab/nsp1128N128EAaTGaA22All0
ORF1ab/nsp1128N128VAAtGTt22All0
ORF1ab/nsp1128N128XAaTTaA22All0
ORF1ab/nsp1128N128NaaTaaC22AY.100.00106
ORF1ab/nsp1128N128TaAtaCt22AY.250.000012
ORF1ab/nsp1128N128NaaTaaC22AY.250.000012
ORF1ab/nsp1128N128DAatGat22AY.290.000032
ORF1ab/nsp1128N128delAAT---22AY.40.000003
ORF1ab/nsp1128N128NaaTaaC22AY.4.20.000043
ORF1ab/nsp1128N128DAatGat22AY.4.2.10.000298
ORF1ab/nsp1128N128NaaTaaC22AY.420.00008
ORF1ab/nsp1128N128delAAT---22AY.430.000009
ORF1ab/nsp1128N128IaAtaTt22AY.440.000012
ORF1ab/nsp1128N128NaaTaaC22AY.450.000243
ORF1ab/nsp1128N128delAAT---22AY.46.60.000144
ORF1ab/nsp1128N128DAatGat22AY.950.001522
ORF1ab/nsp1128N128del1AaT-aN22B.1.10.000036
ORF1ab/nsp1128N128NaaTaaC22B.1.1.280.000622
ORF1ab/nsp1128N128SaAtaGt22B.1.1.3180.000604
ORF1ab/nsp1128N128TaAtaCt22B.1.1.70.000002
ORF1ab/nsp1128N128KaaTaaA22B.1.1.70.000002
ORF1ab/nsp1128N128DAatGat22B.1.1600.000062
ORF1ab/nsp1128N128YAatTat22B.1.20.000018
ORF1ab/nsp1128N128delAAT---22B.1.20.000018
ORF1ab/nsp1128N128del1Aat-at12B.1.20.000009
ORF1ab/nsp1128N128del1aaTaa-12B.1.20.000009
ORF1ab/nsp1128N128VAAtGTt22B.1.2350.005038
ORF1ab/nsp1128N128NaaTaaC22B.1.36.80.002
ORF1ab/nsp1128N128NaaTaaC22B.1.5260.000047
ORF1ab/nsp1128N128TaAtaCt22B.1.617.20.000008
ORF1ab/nsp1128N128delAAT---22N.40.008511
ORF1ab/nsp1128N128delAAT---22N.60.014184
ORF1ab/nsp1128N128delAAT---22P.20.000373
ORF1ab/nsp1128N128QAaTCaA110.055556
ORF1ab/nsp1128N128HAatCat110.055556
ORF1ab/nsp1128N128YAatTat110.055556
ORF1ab/nsp1128N128XAaTTaA110.055556
ORF1ab/nsp1128N128HAatCat11A.10.000282
ORF1ab/nsp1128N128NaaTaaC11A.20.000662
ORF1ab/nsp1128N128QAaTCaA11All0
ORF1ab/nsp1128N128DAatGat11AY.1020.000027
ORF1ab/nsp1128N128SaAtaGt11AY.1020.000027
ORF1ab/nsp1128N128IaAtaTt11AY.1030.000006
ORF1ab/nsp1128N128YAatTat11AY.1030.000006
ORF1ab/nsp1128N128DAatGat11AY.1130.000142
ORF1ab/nsp1128N128delAAT---11AY.1160.000287
ORF1ab/nsp1128N128NaaTaaC11AY.1170.000085
ORF1ab/nsp1128N128delAAT---11AY.120.000316
ORF1ab/nsp1128N128NaaTaaC11AY.1200.000037
ORF1ab/nsp1128N128NaaTaaC11AY.200.000039
ORF1ab/nsp1128N128delAAT---11AY.250.000006
ORF1ab/nsp1128N128GAAtGGt11AY.250.000006
ORF1ab/nsp1128N128LAATCTG11AY.250.000006
ORF1ab/nsp1128N128IaAtaTt11AY.250.000006
ORF1ab/nsp1128N128SaAtaGt11AY.250.000006
ORF1ab/nsp1128N128DAatGat11AY.250.000006
ORF1ab/nsp1128N128YAatTat11AY.250.000006
ORF1ab/nsp1128N128YAatTat11AY.290.000016
ORF1ab/nsp1128N128SaAtaGt11AY.3.10.000085
ORF1ab/nsp1128N128HAatCat11AY.300.000396
ORF1ab/nsp1128N128YAatTat11AY.330.000067
ORF1ab/nsp1128N128NaaTaaC11AY.360.000148
ORF1ab/nsp1128N128delAAT---11AY.380.000499
ORF1ab/nsp1128N128TaAtaCt11AY.390.000025
ORF1ab/nsp1128N128delAAT---11AY.39.10.00004
ORF1ab/nsp1128N128KaaTaaA11AY.40.000002
ORF1ab/nsp1128N128SaAtaGt11AY.4.20.000022
ORF1ab/nsp1128N128DAatGat11AY.4.20.000022
ORF1ab/nsp1128N128SaAtaGt11AY.4.50.000107
ORF1ab/nsp1128N128delAAT---11AY.4.50.000107
ORF1ab/nsp1128N128SaAtaGt11AY.420.00004
ORF1ab/nsp1128N128DAatGat11AY.420.00004
ORF1ab/nsp1128N128SaAtaGt11AY.430.000004
ORF1ab/nsp1128N128YAatTat11AY.430.000004
ORF1ab/nsp1128N128TaAtaCt11AY.430.000004
ORF1ab/nsp1128N128HAatCat11AY.430.000004
ORF1ab/nsp1128N128SaAtaGt11AY.440.000006
ORF1ab/nsp1128N128LAATCTG11AY.440.000006
ORF1ab/nsp1128N128del2aATa--11AY.440.000006
ORF1ab/nsp1128N128YAatTat11AY.440.000006
ORF1ab/nsp1128N128NaaTaaC11AY.460.000104
ORF1ab/nsp1128N128NaaTaaC11AY.470.000031
ORF1ab/nsp1128N128NaaTaaC11AY.50.000021
ORF1ab/nsp1128N128NaaTaaC11AY.600.000938
ORF1ab/nsp1128N128DAatGat11AY.610.000105
ORF1ab/nsp1128N128HAatCat11AY.610.000105
ORF1ab/nsp1128N128delAAT---11AY.650.000533
ORF1ab/nsp1128N128DAatGat11AY.70.000196
ORF1ab/nsp1128N128SaAtaGt11AY.750.000056
ORF1ab/nsp1128N128NaaTaaC11AY.75.10.00018
ORF1ab/nsp1128N128NaaTaaC11AY.770.001127
ORF1ab/nsp1128N128NaaTaaC11AY.80.000606
ORF1ab/nsp1128N128delAAT---11AY.9.10.000084
ORF1ab/nsp1128N128NaaTaaC11AY.9.20.000037
ORF1ab/nsp1128N128delAAT---11AY.950.000761
ORF1ab/nsp1128N128DAatGat11AY.980.000079
ORF1ab/nsp1128N128SaAtaGt11AY.98.10.000048
ORF1ab/nsp1128N128SaAtaGt11AY.99.20.000092
ORF1ab/nsp1128N128GAAtGGt11B.10.000009
ORF1ab/nsp1128N128delAAT---11B.10.000009
ORF1ab/nsp1128N128del1Aat-at11B.10.000009
ORF1ab/nsp1128N128KaaTaaA11B.10.000009
ORF1ab/nsp1128N128KaaTaaG11B.1.10.000018
ORF1ab/nsp1128N128IaAtaTt11B.1.10.000018
ORF1ab/nsp1128N128IaAtaTt11B.1.1.2220.000204
ORF1ab/nsp1128N128DAatGat11B.1.1.2300.009174
ORF1ab/nsp1128N128NaaTaaC11B.1.1.2790.001121
ORF1ab/nsp1128N128NaaTaaC11B.1.1.2850.006536
ORF1ab/nsp1128N128del1aaTaa-11B.1.1.3180.000302
ORF1ab/nsp1128N128NaaTaaC11B.1.1.4290.004608
ORF1ab/nsp1128N128SaAtaGt11B.1.1.5190.00004
ORF1ab/nsp1128N128del1aaTaa-11B.1.1.70.000001
ORF1ab/nsp1128N128IaAtaTt11B.1.1.70.000001
ORF1ab/nsp1128N128YAatTat11B.1.1.70.000001
ORF1ab/nsp1128N128DAatGat11B.1.1.70.000001
ORF1ab/nsp1128N128YAatTat11B.1.1600.000031
ORF1ab/nsp1128N128DAatGat11B.1.1770.000013
ORF1ab/nsp1128N128NaaTaaC11B.1.177.40.000211
ORF1ab/nsp1128N128IaAtaTt11B.1.177.40.000211
ORF1ab/nsp1128N128delAAT---11B.1.177.40.000211
ORF1ab/nsp1128N128del2aATa--11B.1.177.90.001332
ORF1ab/nsp1128N128SaAtaGt11B.1.20.000009
ORF1ab/nsp1128N128del2aATa--11B.1.20.000009
ORF1ab/nsp1128N128IaAtaTt11B.1.20.000009
ORF1ab/nsp1128N128delAAT---11B.1.2110.025
ORF1ab/nsp1128N128del2aATa--11B.1.2210.000071
ORF1ab/nsp1128N128KaaTaaA11B.1.2210.000071
ORF1ab/nsp1128N128NaaTaaC11B.1.2210.000071
ORF1ab/nsp1128N128XAaTTaA11B.1.2210.000071
ORF1ab/nsp1128N128YAatTat11B.1.2210.000071
ORF1ab/nsp1128N128NaaTaaC11B.1.2410.000812
ORF1ab/nsp1128N128NaaTaaC11B.1.3110.000275
ORF1ab/nsp1128N128NaaTaaC11B.1.3510.00003
ORF1ab/nsp1128N128DAatGat11B.1.3510.00003
ORF1ab/nsp1128N128del1AaT-aN11B.1.3550.011111
ORF1ab/nsp1128N128delAAT---11B.1.360.000146
ORF1ab/nsp1128N128NaaTaaC11B.1.4160.001269
ORF1ab/nsp1128N128DAatGat11B.1.4270.00005
ORF1ab/nsp1128N128delAAT---11B.1.4270.00005
ORF1ab/nsp1128N128delAAT---11B.1.4290.000024
ORF1ab/nsp1128N128HAatCat11B.1.4290.000024
ORF1ab/nsp1128N128TaAtaCt11B.1.5260.000024
ORF1ab/nsp1128N128NaaTaaC11B.1.5650.00081
ORF1ab/nsp1128N128del1AaT-aN11B.1.5950.000261
ORF1ab/nsp1128N128DAatGat11B.1.5960.000087
ORF1ab/nsp1128N128delAAT---11B.1.617.20.000004
ORF1ab/nsp1128N128HAatCat11B.1.617.20.000004
ORF1ab/nsp1128N128GAAtGGt11B.1.617.20.000004
ORF1ab/nsp1128N128del1aaTaa-11B.1.617.20.000004
ORF1ab/nsp1128N128KaaTaaA11B.1.617.20.000004
ORF1ab/nsp1128N128KaaTaaA11B.400.000364
ORF1ab/nsp1128N128delAAT---11B.400.000364
ORF1ab/nsp1128N128DAatGat11B.6.60.000889
ORF1ab/nsp1128N128delAAT---11C.170.055556
ORF1ab/nsp1128N128delAAT---11C.350.000774
ORF1ab/nsp1128N128DAatGat11D.20.000075
ORF1ab/nsp1128N128DAatGat11P.10.000016
ORF1ab/nsp1128N128YAatTat11P.10.000016
ORF1ab/nsp1128N128YAatTat11P.1.120.000484
ORF1ab/nsp1128N128IaAtaTt11P.1.170.000162
ORF1ab/nsp1128N128SaAtaGt11Q.30.000145

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.