CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 397

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/nsp4397Y397YY3160YsyntaCtaT8615861519743-9745
ORF1ab/nsp4397Y397HY3160HnonsynTacCac13113119743-9745
ORF1ab/nsp4397Y397CY3160CnonsyntActGc1231220.991879743-9745
ORF1ab/nsp4397Y397CY3160CnonsyntACtGT12310.008130089743-9745
ORF1ab/nsp4397Y397delY3160deldelTAC---10010019743-9745
ORF1ab/nsp4397Y397XY3160XnonsyntaCtaA8819743-9745
ORF1ab/nsp4397Y397FY3160FnonsyntActTc430.759743-9745
ORF1ab/nsp4397Y397FY3160FnonsyntACtTT410.259743-9745
ORF1ab/nsp4397Y397del1Y3160del1delTac-ac320.6666679743-9745
ORF1ab/nsp4397Y397LY3160LnonsyntACtTG320.6666679743-9745
ORF1ab/nsp4397Y397LY3160LnonsyntACtTA310.3333339743-9745
ORF1ab/nsp4397Y397del1Y3160del1deltaCta-310.3333339743-9745
ORF1ab/nsp4397Y397RY3160RnonsynTACAGG2219743-9745
ORF1ab/nsp4397Y397KY3160KnonsynTaCAaG1119743-9745
ORF1ab/nsp4397Y397VY3160VnonsynTACGTA1119743-9745
ORF1ab/nsp4397Y397NY3160NnonsynTacAac1119743-9745
ORF1ab/nsp4397Y397del2Y3160del2delTAc--c1119743-9745
ORF1ab/nsp4397Y397SY3160SnonsyntActCc1119743-9745
ORF1ab/nsp4397Y397TY3160TnonsynTAcACc1119743-9745

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/nsp4397Y397YtaCtaT86158615All0.001648
ORF1ab/nsp4397Y397YtaCtaT35353535B.1.177.570.993257
ORF1ab/nsp4397Y397YtaCtaT16461646B.1.177.540.998181
ORF1ab/nsp4397Y397YtaCtaT14831483B.1.177.560.989987
ORF1ab/nsp4397Y397YtaCtaT427427B.1.177.550.995338
ORF1ab/nsp4397Y397YtaCtaT403403B.1.1.70.000361
ORF1ab/nsp4397Y397HTacCac131131All0.000025
ORF1ab/nsp4397Y397CtActGc122123All0.000023
ORF1ab/nsp4397Y397CtACtGT1123All0
ORF1ab/nsp4397Y397YtaCtaT120120B.1.617.20.000452
ORF1ab/nsp4397Y397YtaCtaT115115P.10.001812
ORF1ab/nsp4397Y397delTAC---100100All0.000019
ORF1ab/nsp4397Y397YtaCtaT9696AY.430.000425
ORF1ab/nsp4397Y397YtaCtaT8181AY.40.000126
ORF1ab/nsp4397Y397YtaCtaT5858B.1.1770.000764
ORF1ab/nsp4397Y397YtaCtaT5858C.40.58
ORF1ab/nsp4397Y397YtaCtaT4646B.1.1.5190.001827
ORF1ab/nsp4397Y397delTAC---4545B.1.1.70.00004
ORF1ab/nsp4397Y397YtaCtaT4444V.11
ORF1ab/nsp4397Y397HTacCac4141B.1.6161
ORF1ab/nsp4397Y397YtaCtaT3939B.10.000357
ORF1ab/nsp4397Y397YtaCtaT3636AY.116.10.011211
ORF1ab/nsp4397Y397YtaCtaT3333B.1.5850.916667
ORF1ab/nsp4397Y397YtaCtaT3030V.20.967742
ORF1ab/nsp4397Y397YtaCtaT2626B.1.1.3170.010704
ORF1ab/nsp4397Y397HTacCac2626B.1.2210.001847
ORF1ab/nsp4397Y397CtActGc2525B.1.2210.001776
ORF1ab/nsp4397Y397YtaCtaT2121AY.5.40.005811
ORF1ab/nsp4397Y397YtaCtaT1919AY.34.10.009689
ORF1ab/nsp4397Y397YtaCtaT1919B.1.20.000167
ORF1ab/nsp4397Y397YtaCtaT1818AY.1030.000112
ORF1ab/nsp4397Y397YtaCtaT1616B.1.6280.005638
ORF1ab/nsp4397Y397CtActGc1515B.1.2430.001044
ORF1ab/nsp4397Y397YtaCtaT1414B.1.177.180.016241
ORF1ab/nsp4397Y397YtaCtaT1313AY.390.000321
ORF1ab/nsp4397Y397CtActGc1313B.1.10.000236
ORF1ab/nsp4397Y397CtActGc1313B.1.4740.024715
ORF1ab/nsp4397Y397YtaCtaT1212AY.440.000073
ORF1ab/nsp4397Y397YtaCtaT1212B.1.6370.000877
ORF1ab/nsp4397Y397YtaCtaT1111AY.250.000066
ORF1ab/nsp4397Y397YtaCtaT1111B.1.10.0002
ORF1ab/nsp4397Y397HTacCac1111B.1.20.000097
ORF1ab/nsp4397Y397delTAC---99B.1.1770.000119
ORF1ab/nsp4397Y397CtActGc99D.20.000675
ORF1ab/nsp4397Y397XtaCtaA88All0.000002
ORF1ab/nsp4397Y397YtaCtaT88B.1.160.160.007435
ORF1ab/nsp4397Y397delTAC---77AY.40.000011
ORF1ab/nsp4397Y397delTAC---77AY.4.50.000752
ORF1ab/nsp4397Y397YtaCtaT77AY.50.000145
ORF1ab/nsp4397Y397YtaCtaT77AY.5.30.002362
ORF1ab/nsp4397Y397CtActGc77B.1.20.000062
ORF1ab/nsp4397Y397YtaCtaT66B.1.3510.000178
ORF1ab/nsp4397Y397YtaCtaT66B.1.5770.004124
ORF1ab/nsp4397Y397YtaCtaT55AY.470.000156
ORF1ab/nsp4397Y397HTacCac55B0.000639
ORF1ab/nsp4397Y397HTacCac55B.1.1.280.001556
ORF1ab/nsp4397Y397HTacCac55B.1.1420.014493
ORF1ab/nsp4397Y397CtActGc55L.30.01773
ORF1ab/nsp4397Y397FtActTc34All0.000001
ORF1ab/nsp4397Y397FtACtTT14All0
ORF1ab/nsp4397Y397YtaCtaT44AY.260.000113
ORF1ab/nsp4397Y397YtaCtaT44AY.30.00004
ORF1ab/nsp4397Y397YtaCtaT44AY.370.001264
ORF1ab/nsp4397Y397delTAC---44AY.430.000018
ORF1ab/nsp4397Y397YtaCtaT44AY.99.20.000369
ORF1ab/nsp4397Y397YtaCtaT44B.1.1.10.001307
ORF1ab/nsp4397Y397YtaCtaT44B.1.2580.000266
ORF1ab/nsp4397Y397YtaCtaT44B.1.6210.000354
ORF1ab/nsp4397Y397CtActGc44B.400.001457
ORF1ab/nsp4397Y397YtaCtaT44C.370.000464
ORF1ab/nsp4397Y397XtaCtaA330.166667
ORF1ab/nsp4397Y397LtACtTG23All0
ORF1ab/nsp4397Y397del1Tac-ac23All0
ORF1ab/nsp4397Y397del1taCta-13All0
ORF1ab/nsp4397Y397LtACtTA13All0
ORF1ab/nsp4397Y397HTacCac33AY.50.000062
ORF1ab/nsp4397Y397YtaCtaT33AY.530.000863
ORF1ab/nsp4397Y397YtaCtaT33AY.70.000588
ORF1ab/nsp4397Y397YtaCtaT33AY.90.000203
ORF1ab/nsp4397Y397CtActGc33B.10.000027
ORF1ab/nsp4397Y397CtActGc33B.1.1770.00004
ORF1ab/nsp4397Y397CtActGc33B.1.3990.005803
ORF1ab/nsp4397Y397YtaCtaT33B.1.5610.001191
ORF1ab/nsp4397Y397YtaCtaT33P.1.140.000143
ORF1ab/nsp4397Y397YtaCtaT33Q.40.001364
ORF1ab/nsp4397Y397CtActGc220.111111
ORF1ab/nsp4397Y397LtACtTG220.111111
ORF1ab/nsp4397Y397RTACAGG220.111111
ORF1ab/nsp4397Y397YtaCtaT22A.190.018868
ORF1ab/nsp4397Y397RTACAGG22All0
ORF1ab/nsp4397Y397YtaCtaT22AY.1020.000053
ORF1ab/nsp4397Y397YtaCtaT22AY.1190.000071
ORF1ab/nsp4397Y397HTacCac22AY.30.00002
ORF1ab/nsp4397Y397YtaCtaT22AY.330.000134
ORF1ab/nsp4397Y397YtaCtaT22AY.39.10.000079
ORF1ab/nsp4397Y397YtaCtaT22AY.4.20.000043
ORF1ab/nsp4397Y397YtaCtaT22AY.46.20.001271
ORF1ab/nsp4397Y397delTAC---22AY.99.10.003106
ORF1ab/nsp4397Y397CtActGc22B0.000256
ORF1ab/nsp4397Y397XtaCtaA22B.10.000018
ORF1ab/nsp4397Y397YtaCtaT22B.1.1.1900.1
ORF1ab/nsp4397Y397CtActGc22B.1.1.2160.001781
ORF1ab/nsp4397Y397YtaCtaT22B.1.1.2220.000408
ORF1ab/nsp4397Y397YtaCtaT22B.1.1.3060.000877
ORF1ab/nsp4397Y397CtActGc22B.1.1.5190.000079
ORF1ab/nsp4397Y397HTacCac22B.1.1.70.000002
ORF1ab/nsp4397Y397CtActGc22B.1.1600.000062
ORF1ab/nsp4397Y397HTacCac22B.1.1600.000062
ORF1ab/nsp4397Y397HTacCac22B.1.1770.000026
ORF1ab/nsp4397Y397YtaCtaT22B.1.177.110.003396
ORF1ab/nsp4397Y397delTAC---22B.1.177.40.000422
ORF1ab/nsp4397Y397HTacCac22B.1.177.80.001505
ORF1ab/nsp4397Y397delTAC---22B.1.20.000018
ORF1ab/nsp4397Y397YtaCtaT22B.1.2390.002442
ORF1ab/nsp4397Y397YtaCtaT22B.1.36.260.005714
ORF1ab/nsp4397Y397YtaCtaT22B.1.4250.005988
ORF1ab/nsp4397Y397YtaCtaT22B.1.4260.002018
ORF1ab/nsp4397Y397CtActGc22B.1.5050.008772
ORF1ab/nsp4397Y397HTacCac22B.1.5090.001732
ORF1ab/nsp4397Y397CtActGc22B.1.5770.001375
ORF1ab/nsp4397Y397YtaCtaT22B.1.5950.000522
ORF1ab/nsp4397Y397YtaCtaT22B.1.6230.001073
ORF1ab/nsp4397Y397HTacCac22B.400.000729
ORF1ab/nsp4397Y397HTacCac22D.20.00015
ORF1ab/nsp4397Y397YtaCtaT11A0.000387
ORF1ab/nsp4397Y397delTAC---11AD.20.000219
ORF1ab/nsp4397Y397StActCc11All0
ORF1ab/nsp4397Y397TTAcACc11All0
ORF1ab/nsp4397Y397del2TAc--c11All0
ORF1ab/nsp4397Y397VTACGTA11All0
ORF1ab/nsp4397Y397NTacAac11All0
ORF1ab/nsp4397Y397KTaCAaG11All0
ORF1ab/nsp4397Y397YtaCtaT11AY.1160.000287
ORF1ab/nsp4397Y397YtaCtaT11AY.1170.000085
ORF1ab/nsp4397Y397HTacCac11AY.1200.000037
ORF1ab/nsp4397Y397YtaCtaT11AY.160.00038
ORF1ab/nsp4397Y397delTAC---11AY.190.00114
ORF1ab/nsp4397Y397YtaCtaT11AY.200.000039
ORF1ab/nsp4397Y397YtaCtaT11AY.230.00007
ORF1ab/nsp4397Y397XtaCtaA11AY.250.000006
ORF1ab/nsp4397Y397HTacCac11AY.250.000006
ORF1ab/nsp4397Y397YtaCtaT11AY.290.000016
ORF1ab/nsp4397Y397HTacCac11AY.39.10.00004
ORF1ab/nsp4397Y397delTAC---11AY.4.30.000842
ORF1ab/nsp4397Y397YtaCtaT11AY.420.00004
ORF1ab/nsp4397Y397HTacCac11AY.430.000004
ORF1ab/nsp4397Y397FtActTc11AY.46.20.000635
ORF1ab/nsp4397Y397HTacCac11AY.46.60.000072
ORF1ab/nsp4397Y397YtaCtaT11AY.46.60.000072
ORF1ab/nsp4397Y397delTAC---11AY.60.000041
ORF1ab/nsp4397Y397YtaCtaT11AY.620.000436
ORF1ab/nsp4397Y397HTacCac11AY.670.000464
ORF1ab/nsp4397Y397YtaCtaT11AY.680.000274
ORF1ab/nsp4397Y397delTAC---11AY.680.000274
ORF1ab/nsp4397Y397YtaCtaT11AY.710.000475
ORF1ab/nsp4397Y397YtaCtaT11AY.750.000056
ORF1ab/nsp4397Y397YtaCtaT11AY.75.10.00018
ORF1ab/nsp4397Y397CtActGc11AY.790.001211
ORF1ab/nsp4397Y397delTAC---11AY.90.000068
ORF1ab/nsp4397Y397YtaCtaT11AY.9.10.000084
ORF1ab/nsp4397Y397YtaCtaT11AY.9.20.000037
ORF1ab/nsp4397Y397YtaCtaT11AY.980.000079
ORF1ab/nsp4397Y397delTAC---11AY.990.001049
ORF1ab/nsp4397Y397YtaCtaT11B0.000128
ORF1ab/nsp4397Y397HTacCac11B.10.000009
ORF1ab/nsp4397Y397TTAcACc11B.10.000009
ORF1ab/nsp4397Y397StActCc11B.10.000009
ORF1ab/nsp4397Y397delTAC---11B.1.10.000018
ORF1ab/nsp4397Y397XtaCtaA11B.1.10.000018
ORF1ab/nsp4397Y397KTaCAaG11B.1.10.000018
ORF1ab/nsp4397Y397FtActTc11B.1.10.000018
ORF1ab/nsp4397Y397LtACtTA11B.1.10.000018
ORF1ab/nsp4397Y397del1Tac-ac11B.1.1.1390.022727
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.1410.002012
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.2140.000055
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.3110.000358
ORF1ab/nsp4397Y397delTAC---11B.1.1.370.000193
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.370.000193
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.3720.000689
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.410.006329
ORF1ab/nsp4397Y397HTacCac11B.1.1.4340.000349
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.4340.000349
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.4640.001473
ORF1ab/nsp4397Y397HTacCac11B.1.1.4830.038462
ORF1ab/nsp4397Y397YtaCtaT11B.1.1.4870.005587
ORF1ab/nsp4397Y397del2TAc--c11B.1.1.70.000001
ORF1ab/nsp4397Y397FtACtTT11B.1.1.70.000001
ORF1ab/nsp4397Y397delTAC---11B.1.1.700.000341
ORF1ab/nsp4397Y397CtActGc11B.1.1.80.003584
ORF1ab/nsp4397Y397YtaCtaT11B.1.130.002375
ORF1ab/nsp4397Y397YtaCtaT11B.1.1600.000031
ORF1ab/nsp4397Y397del1Tac-ac11B.1.1770.000013
ORF1ab/nsp4397Y397delTAC---11B.1.177.110.001698
ORF1ab/nsp4397Y397YtaCtaT11B.1.177.160.000664
ORF1ab/nsp4397Y397delTAC---11B.1.177.170.000821
ORF1ab/nsp4397Y397HTacCac11B.1.177.210.000076
ORF1ab/nsp4397Y397YtaCtaT11B.1.177.40.000211
ORF1ab/nsp4397Y397HTacCac11B.1.177.530.002392
ORF1ab/nsp4397Y397CtACtGT11B.1.177.550.002331
ORF1ab/nsp4397Y397delTAC---11B.1.177.560.000668
ORF1ab/nsp4397Y397delTAC---11B.1.177.580.001332
ORF1ab/nsp4397Y397delTAC---11B.1.177.690.001484
ORF1ab/nsp4397Y397delTAC---11B.1.177.760.002494
ORF1ab/nsp4397Y397CtActGc11B.1.177.80.000752
ORF1ab/nsp4397Y397YtaCtaT11B.1.177.820.000477
ORF1ab/nsp4397Y397YtaCtaT11B.1.177.860.000183
ORF1ab/nsp4397Y397HTacCac11B.1.2290.009709
ORF1ab/nsp4397Y397YtaCtaT11B.1.2340.000132
ORF1ab/nsp4397Y397YtaCtaT11B.1.2400.000216
ORF1ab/nsp4397Y397delTAC---11B.1.258.30.001675
ORF1ab/nsp4397Y397YtaCtaT11B.1.3240.001605
ORF1ab/nsp4397Y397del1taCta-11B.1.3510.00003
ORF1ab/nsp4397Y397NTacAac11B.1.3510.00003
ORF1ab/nsp4397Y397YtaCtaT11B.1.351.30.000876
ORF1ab/nsp4397Y397CtActGc11B.1.3560.001727
ORF1ab/nsp4397Y397YtaCtaT11B.1.36.170.000494
ORF1ab/nsp4397Y397delTAC---11B.1.36.380.001642
ORF1ab/nsp4397Y397CtActGc11B.1.3710.001122
ORF1ab/nsp4397Y397HTacCac11B.1.3960.000706
ORF1ab/nsp4397Y397CtActGc11B.1.416.10.001563
ORF1ab/nsp4397Y397CtActGc11B.1.4290.000024
ORF1ab/nsp4397Y397HTacCac11B.1.4290.000024
ORF1ab/nsp4397Y397YtaCtaT11B.1.466.20.000391
ORF1ab/nsp4397Y397YtaCtaT11B.1.4700.001404
ORF1ab/nsp4397Y397YtaCtaT11B.1.5260.000024
ORF1ab/nsp4397Y397YtaCtaT11B.1.5400.009709
ORF1ab/nsp4397Y397YtaCtaT11B.1.575.10.002439
ORF1ab/nsp4397Y397HTacCac11B.1.5760.000907
ORF1ab/nsp4397Y397XtaCtaA11B.1.5800.004065
ORF1ab/nsp4397Y397YtaCtaT11B.1.5970.00463
ORF1ab/nsp4397Y397VTACGTA11B.1.617.10.000129
ORF1ab/nsp4397Y397delTAC---11B.1.617.10.000129
ORF1ab/nsp4397Y397delTAC---11B.1.617.20.000004
ORF1ab/nsp4397Y397CtActGc11B.1.810.021277
ORF1ab/nsp4397Y397HTacCac11B.390.002331
ORF1ab/nsp4397Y397HTacCac11B.4.60.016667
ORF1ab/nsp4397Y397YtaCtaT11B.450.003831
ORF1ab/nsp4397Y397HTacCac11B.60.00091
ORF1ab/nsp4397Y397HTacCac11C.350.000774
ORF1ab/nsp4397Y397FtActTc11D.20.000075
ORF1ab/nsp4397Y397YtaCtaT11P.1.150.000232
ORF1ab/nsp4397Y397YtaCtaT11P.1.17.10.000875
ORF1ab/nsp4397Y397YtaCtaT11P.1.70.000319
ORF1ab/nsp4397Y397delTAC---11Q.10.000126
ORF1ab/nsp4397Y397YtaCtaT11Q.80.000165
ORF1ab/nsp4397Y397YtaCtaT11R.10.00009
ORF1ab/nsp4397Y397delTAC---11U.30.003861

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.