CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 304

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/nsp12304D304DD4696DsyngaCgaT544544114350-14352
ORF1ab/nsp12304D304YD4696YnonsynGacTac543543114350-14352
ORF1ab/nsp12304D304delD4696deldelGAC---123123114350-14352
ORF1ab/nsp12304D304GD4696GnonsyngAcgGc9393114350-14352
ORF1ab/nsp12304D304ND4696NnonsynGacAac29260.89655214350-14352
ORF1ab/nsp12304D304ND4696NnonsynGaCAaT2930.10344814350-14352
ORF1ab/nsp12304D304HD4696HnonsynGacCac88114350-14352
ORF1ab/nsp12304D304ED4696EnonsyngaCgaA870.87514350-14352
ORF1ab/nsp12304D304AD4696AnonsyngAcgCc870.87514350-14352
ORF1ab/nsp12304D304AD4696AnonsyngACgCA810.12514350-14352
ORF1ab/nsp12304D304ED4696EnonsyngaCgaG810.12514350-14352
ORF1ab/nsp12304D304del2D4696del2delGAc--c33114350-14352
ORF1ab/nsp12304D304SD4696SnonsynGACAGT33114350-14352
ORF1ab/nsp12304D304VD4696VnonsyngAcgTc320.66666714350-14352
ORF1ab/nsp12304D304VD4696VnonsyngACgTA310.33333314350-14352
ORF1ab/nsp12304D304del1D4696del1delGaC-aT22114350-14352
ORF1ab/nsp12304D304TD4696TnonsynGACACG11114350-14352
ORF1ab/nsp12304D304PD4696PnonsynGACCCT11114350-14352

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/nsp12304D304DgaCgaT544544All0.000104
ORF1ab/nsp12304D304YGacTac543543All0.000104
ORF1ab/nsp12304D304DgaCgaT247247B.1.1.70.000221
ORF1ab/nsp12304D304YGacTac155155AY.430.000687
ORF1ab/nsp12304D304delGAC---123123All0.000024
ORF1ab/nsp12304D304YGacTac107107B.1.617.20.000403
ORF1ab/nsp12304D304GgAcgGc9393All0.000018
ORF1ab/nsp12304D304delGAC---6565B.1.1.70.000058
ORF1ab/nsp12304D304DgaCgaT4949AN.10.98
ORF1ab/nsp12304D304GgAcgGc4141B.1.617.20.000154
ORF1ab/nsp12304D304YGacTac3535A.10.009865
ORF1ab/nsp12304D304YGacTac3131AY.250.000186
ORF1ab/nsp12304D304DgaCgaT3131AY.40.000048
ORF1ab/nsp12304D304NGacAac2629All0.000005
ORF1ab/nsp12304D304NGaCAaT329All0.000001
ORF1ab/nsp12304D304DgaCgaT2929B.1.4270.001464
ORF1ab/nsp12304D304YGacTac2424AY.50.000496
ORF1ab/nsp12304D304YGacTac1919B.1.1.3520.59375
ORF1ab/nsp12304D304YGacTac1717AY.40.000026
ORF1ab/nsp12304D304DgaCgaT1717B.1.617.20.000064
ORF1ab/nsp12304D304GgAcgGc1515AY.40.000023
ORF1ab/nsp12304D304YGacTac1515B.1.1.70.000013
ORF1ab/nsp12304D304YGacTac1414AY.4.10.010324
ORF1ab/nsp12304D304YGacTac1313AY.330.000868
ORF1ab/nsp12304D304YGacTac1313B.10.000119
ORF1ab/nsp12304D304GgAcgGc1111AY.290.000174
ORF1ab/nsp12304D304delGAC---1111AY.40.000017
ORF1ab/nsp12304D304NGacAac1111AY.40.000017
ORF1ab/nsp12304D304DgaCgaT1111AY.430.000049
ORF1ab/nsp12304D304DgaCgaT1111B.10.000101
ORF1ab/nsp12304D304DgaCgaT99AY.1200.000335
ORF1ab/nsp12304D304DgaCgaT99P.10.000142
ORF1ab/nsp12304D304HGacCac88All0.000002
ORF1ab/nsp12304D304EgaCgaA78All0.000001
ORF1ab/nsp12304D304AgAcgCc78All0.000001
ORF1ab/nsp12304D304AgACgCA18All0
ORF1ab/nsp12304D304EgaCgaG18All0
ORF1ab/nsp12304D304DgaCgaT88B.1.10.000145
ORF1ab/nsp12304D304DgaCgaT88B.1.2580.000532
ORF1ab/nsp12304D304YGacTac88D.20.0006
ORF1ab/nsp12304D304YGacTac77AY.390.000173
ORF1ab/nsp12304D304DgaCgaT77B.1.1600.000218
ORF1ab/nsp12304D304DgaCgaT66AY.1030.000037
ORF1ab/nsp12304D304delGAC---66AY.430.000027
ORF1ab/nsp12304D304DgaCgaT66AY.440.000037
ORF1ab/nsp12304D304DgaCgaT66B.1.20.000053
ORF1ab/nsp12304D304DgaCgaT55AY.250.00003
ORF1ab/nsp12304D304delGAC---55AY.250.00003
ORF1ab/nsp12304D304DgaCgaT55AY.370.00158
ORF1ab/nsp12304D304delGAC---55AY.4.50.000537
ORF1ab/nsp12304D304YGacTac55AY.460.00052
ORF1ab/nsp12304D304NGacAac45B.1.1.70.000004
ORF1ab/nsp12304D304NGaCAaT15B.1.1.70.000001
ORF1ab/nsp12304D304YGacTac55B.1.5260.000118
ORF1ab/nsp12304D304YGacTac44AY.1020.000106
ORF1ab/nsp12304D304YGacTac44AY.1060.00134
ORF1ab/nsp12304D304DgaCgaT44AY.230.000279
ORF1ab/nsp12304D304GgAcgGc44AY.260.000113
ORF1ab/nsp12304D304DgaCgaT44AY.30.00004
ORF1ab/nsp12304D304DgaCgaT44AY.300.001583
ORF1ab/nsp12304D304NGacAac44AY.4.50.00043
ORF1ab/nsp12304D304GgAcgGc44B.1.1.70.000004
ORF1ab/nsp12304D304YGacTac44B.1.20.000035
ORF1ab/nsp12304D304del2GAc--c33All0.000001
ORF1ab/nsp12304D304SGACAGT33All0.000001
ORF1ab/nsp12304D304VgAcgTc23All0
ORF1ab/nsp12304D304VgACgTA13All0
ORF1ab/nsp12304D304DgaCgaT33AY.140.000264
ORF1ab/nsp12304D304AgAcgCc33AY.250.000018
ORF1ab/nsp12304D304YGacTac33AY.290.000047
ORF1ab/nsp12304D304YGacTac33AY.3.10.000256
ORF1ab/nsp12304D304DgaCgaT33AY.390.000074
ORF1ab/nsp12304D304YGacTac33AY.440.000018
ORF1ab/nsp12304D304DgaCgaT33AY.750.000168
ORF1ab/nsp12304D304YGacTac33AY.98.10.000145
ORF1ab/nsp12304D304DgaCgaT33B0.000383
ORF1ab/nsp12304D304YGacTac33B.1.1.2580.009772
ORF1ab/nsp12304D304delGAC---33B.1.1770.00004
ORF1ab/nsp12304D304SGACAGT220.111111
ORF1ab/nsp12304D304delGAC---220.111111
ORF1ab/nsp12304D304EgaCgaA220.111111
ORF1ab/nsp12304D304del1GaC-aT22All0
ORF1ab/nsp12304D304GgAcgGc22AY.1100.000225
ORF1ab/nsp12304D304DgaCgaT22AY.1180.000125
ORF1ab/nsp12304D304YGacTac22AY.1210.000271
ORF1ab/nsp12304D304YGacTac22AY.230.000139
ORF1ab/nsp12304D304YGacTac22AY.30.00002
ORF1ab/nsp12304D304DgaCgaT22AY.3.10.000171
ORF1ab/nsp12304D304YGacTac22AY.4.20.000043
ORF1ab/nsp12304D304GgAcgGc22AY.4.50.000215
ORF1ab/nsp12304D304DgaCgaT22AY.450.000243
ORF1ab/nsp12304D304DgaCgaT22AY.46.40.000329
ORF1ab/nsp12304D304YGacTac22AY.46.60.000144
ORF1ab/nsp12304D304YGacTac22AY.5.40.000553
ORF1ab/nsp12304D304delGAC---22B.10.000018
ORF1ab/nsp12304D304HGacCac22B.10.000018
ORF1ab/nsp12304D304YGacTac22B.1.10.000036
ORF1ab/nsp12304D304EgaCgaA22B.1.10.000036
ORF1ab/nsp12304D304YGacTac22B.1.1.5190.000079
ORF1ab/nsp12304D304DgaCgaT22B.1.1.5190.000079
ORF1ab/nsp12304D304GgAcgGc22B.1.20.000018
ORF1ab/nsp12304D304YGacTac22B.1.2210.000142
ORF1ab/nsp12304D304DgaCgaT22B.1.2430.000139
ORF1ab/nsp12304D304DgaCgaT22B.1.360.000292
ORF1ab/nsp12304D304DgaCgaT22B.1.36.80.002
ORF1ab/nsp12304D304DgaCgaT22B.1.5750.000607
ORF1ab/nsp12304D304DgaCgaT22B.1.5960.000174
ORF1ab/nsp12304D304DgaCgaT22B.1.6370.000146
ORF1ab/nsp12304D304DgaCgaT22P.1.140.000096
ORF1ab/nsp12304D304DgaCgaT22P.20.000373
ORF1ab/nsp12304D304VgACgTA11AE.30.032258
ORF1ab/nsp12304D304PGACCCT11All0
ORF1ab/nsp12304D304TGACACG11All0
ORF1ab/nsp12304D304GgAcgGc11AY.1030.000006
ORF1ab/nsp12304D304YGacTac11AY.1030.000006
ORF1ab/nsp12304D304AgAcgCc11AY.1030.000006
ORF1ab/nsp12304D304YGacTac11AY.1100.000113
ORF1ab/nsp12304D304delGAC---11AY.1110.000183
ORF1ab/nsp12304D304GgAcgGc11AY.1130.000142
ORF1ab/nsp12304D304HGacCac11AY.1180.000063
ORF1ab/nsp12304D304AgAcgCc11AY.1180.000063
ORF1ab/nsp12304D304DgaCgaT11AY.1190.000035
ORF1ab/nsp12304D304GgAcgGc11AY.1190.000035
ORF1ab/nsp12304D304AgAcgCc11AY.1200.000037
ORF1ab/nsp12304D304delGAC---11AY.190.00114
ORF1ab/nsp12304D304YGacTac11AY.200.000039
ORF1ab/nsp12304D304GgAcgGc11AY.250.000006
ORF1ab/nsp12304D304delGAC---11AY.290.000016
ORF1ab/nsp12304D304NGacAac11AY.290.000016
ORF1ab/nsp12304D304DgaCgaT11AY.290.000016
ORF1ab/nsp12304D304delGAC---11AY.30.00001
ORF1ab/nsp12304D304DgaCgaT11AY.34.10.00051
ORF1ab/nsp12304D304GgAcgGc11AY.390.000025
ORF1ab/nsp12304D304DgaCgaT11AY.4.20.000022
ORF1ab/nsp12304D304YGacTac11AY.4.40.000409
ORF1ab/nsp12304D304DgaCgaT11AY.4.50.000107
ORF1ab/nsp12304D304DgaCgaT11AY.420.00004
ORF1ab/nsp12304D304YGacTac11AY.420.00004
ORF1ab/nsp12304D304del1GaC-aT11AY.430.000004
ORF1ab/nsp12304D304HGacCac11AY.430.000004
ORF1ab/nsp12304D304GgAcgGc11AY.440.000006
ORF1ab/nsp12304D304YGacTac11AY.470.000031
ORF1ab/nsp12304D304GgAcgGc11AY.540.000095
ORF1ab/nsp12304D304YGacTac11AY.560.001605
ORF1ab/nsp12304D304YGacTac11AY.590.00053
ORF1ab/nsp12304D304GgAcgGc11AY.590.00053
ORF1ab/nsp12304D304DgaCgaT11AY.60.000041
ORF1ab/nsp12304D304YGacTac11AY.60.000041
ORF1ab/nsp12304D304YGacTac11AY.610.000105
ORF1ab/nsp12304D304NGaCAaT11AY.610.000105
ORF1ab/nsp12304D304DgaCgaT11AY.620.000436
ORF1ab/nsp12304D304DgaCgaT11AY.650.000533
ORF1ab/nsp12304D304delGAC---11AY.670.000464
ORF1ab/nsp12304D304delGAC---11AY.720.001361
ORF1ab/nsp12304D304DgaCgaT11AY.75.10.00018
ORF1ab/nsp12304D304NGaCAaT11AY.840.000437
ORF1ab/nsp12304D304delGAC---11AY.850.000427
ORF1ab/nsp12304D304DgaCgaT11AY.90.000068
ORF1ab/nsp12304D304delGAC---11AY.9.20.000037
ORF1ab/nsp12304D304YGacTac11AY.930.000273
ORF1ab/nsp12304D304DgaCgaT11AY.960.002075
ORF1ab/nsp12304D304DgaCgaT11AY.98.10.000048
ORF1ab/nsp12304D304del1GaC-aT11AY.990.001049
ORF1ab/nsp12304D304YGacTac11AY.99.20.000092
ORF1ab/nsp12304D304NGacAac11B0.000128
ORF1ab/nsp12304D304YGacTac11B0.000128
ORF1ab/nsp12304D304NGacAac11B.10.000009
ORF1ab/nsp12304D304delGAC---11B.1.10.000018
ORF1ab/nsp12304D304NGacAac11B.1.10.000018
ORF1ab/nsp12304D304GgAcgGc11B.1.1.10.000327
ORF1ab/nsp12304D304YGacTac11B.1.1.1410.002012
ORF1ab/nsp12304D304YGacTac11B.1.1.1860.003436
ORF1ab/nsp12304D304YGacTac11B.1.1.2050.003717
ORF1ab/nsp12304D304YGacTac11B.1.1.2200.001859
ORF1ab/nsp12304D304delGAC---11B.1.1.2210.010101
ORF1ab/nsp12304D304DgaCgaT11B.1.1.2220.000204
ORF1ab/nsp12304D304YGacTac11B.1.1.2220.000204
ORF1ab/nsp12304D304delGAC---11B.1.1.2320.001815
ORF1ab/nsp12304D304YGacTac11B.1.1.3060.000438
ORF1ab/nsp12304D304DgaCgaT11B.1.1.3060.000438
ORF1ab/nsp12304D304del2GAc--c11B.1.1.3110.000358
ORF1ab/nsp12304D304DgaCgaT11B.1.1.3180.000302
ORF1ab/nsp12304D304GgAcgGc11B.1.1.3660.015873
ORF1ab/nsp12304D304delGAC---11B.1.1.370.000193
ORF1ab/nsp12304D304DgaCgaT11B.1.1.390.00051
ORF1ab/nsp12304D304GgAcgGc11B.1.1.3980.003226
ORF1ab/nsp12304D304HGacCac11B.1.1.5190.00004
ORF1ab/nsp12304D304HGacCac11B.1.1.70.000001
ORF1ab/nsp12304D304TGACACG11B.1.1.70.000001
ORF1ab/nsp12304D304SGACAGT11B.1.1.70.000001
ORF1ab/nsp12304D304AgAcgCc11B.1.1.70.000001
ORF1ab/nsp12304D304delGAC---11B.1.1.700.000341
ORF1ab/nsp12304D304DgaCgaT11B.1.1530.018868
ORF1ab/nsp12304D304DgaCgaT11B.1.1730.026316
ORF1ab/nsp12304D304NGacAac11B.1.1770.000013
ORF1ab/nsp12304D304DgaCgaT11B.1.1770.000013
ORF1ab/nsp12304D304YGacTac11B.1.1770.000013
ORF1ab/nsp12304D304YGacTac11B.1.177.170.000821
ORF1ab/nsp12304D304delGAC---11B.1.177.180.00116
ORF1ab/nsp12304D304delGAC---11B.1.177.540.000606
ORF1ab/nsp12304D304YGacTac11B.1.177.70.000165
ORF1ab/nsp12304D304NGacAac11B.1.177.710.010101
ORF1ab/nsp12304D304YGacTac11B.1.177.740.015152
ORF1ab/nsp12304D304YGacTac11B.1.177.850.005435
ORF1ab/nsp12304D304delGAC---11B.1.177.870.000728
ORF1ab/nsp12304D304del2GAc--c11B.1.177.90.001332
ORF1ab/nsp12304D304YGacTac11B.1.1880.016667
ORF1ab/nsp12304D304delGAC---11B.1.230.006061
ORF1ab/nsp12304D304del2GAc--c11B.1.258.30.001675
ORF1ab/nsp12304D304NGacAac11B.1.3110.000275
ORF1ab/nsp12304D304DgaCgaT11B.1.3290.000608
ORF1ab/nsp12304D304DgaCgaT11B.1.3510.00003
ORF1ab/nsp12304D304AgACgCA11B.1.360.000146
ORF1ab/nsp12304D304EgaCgaA11B.1.36.170.000494
ORF1ab/nsp12304D304delGAC---11B.1.36.170.000494
ORF1ab/nsp12304D304delGAC---11B.1.36.290.000517
ORF1ab/nsp12304D304EgaCgaA11B.1.3670.000792
ORF1ab/nsp12304D304DgaCgaT11B.1.3690.000285
ORF1ab/nsp12304D304delGAC---11B.1.5250.000113
ORF1ab/nsp12304D304DgaCgaT11B.1.5610.000397
ORF1ab/nsp12304D304YGacTac11B.1.5680.001111
ORF1ab/nsp12304D304EgaCgaG11B.1.5950.000261
ORF1ab/nsp12304D304EgaCgaA11B.1.5960.000087
ORF1ab/nsp12304D304HGacCac11B.1.5960.000087
ORF1ab/nsp12304D304VgAcgTc11B.1.5960.000087
ORF1ab/nsp12304D304YGacTac11B.1.6000.005848
ORF1ab/nsp12304D304VgAcgTc11B.1.617.20.000004
ORF1ab/nsp12304D304DgaCgaT11B.1.6210.000089
ORF1ab/nsp12304D304PGACCCT11B.1.6210.000089
ORF1ab/nsp12304D304delGAC---11B.1.6210.000089
ORF1ab/nsp12304D304YGacTac11B.1.6270.00202
ORF1ab/nsp12304D304DgaCgaT11B.1.6360.006711
ORF1ab/nsp12304D304YGacTac11B.30.000831
ORF1ab/nsp12304D304GgAcgGc11B.60.00091
ORF1ab/nsp12304D304HGacCac11D.20.000075
ORF1ab/nsp12304D304YGacTac11P.10.000016
ORF1ab/nsp12304D304delGAC---11P.1.10.000318
ORF1ab/nsp12304D304DgaCgaT11P.1.10.000318
ORF1ab/nsp12304D304delGAC---11P.1.100.000269
ORF1ab/nsp12304D304DgaCgaT11P.1.130.000898
ORF1ab/nsp12304D304DgaCgaT11P.1.170.000162
ORF1ab/nsp12304D304delGAC---11Q.20.000613
ORF1ab/nsp12304D304DgaCgaT11Q.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.