CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1042

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/nsp31042K1042EK1860EnonsynAaaGaa24924915843-5845
ORF1ab/nsp31042K1042KK1860KsynaaAaaG20620615843-5845
ORF1ab/nsp31042K1042NK1860NnonsynaaAaaT1911300.6806285843-5845
ORF1ab/nsp31042K1042NK1860NnonsynaaAaaC191610.3193725843-5845
ORF1ab/nsp31042K1042RK1860RnonsynaAaaGa959515843-5845
ORF1ab/nsp31042K1042TK1860TnonsynaAaaCa595915843-5845
ORF1ab/nsp31042K1042delK1860deldelAAA---161615843-5845
ORF1ab/nsp31042K1042IK1860InonsynaAaaTa141415843-5845
ORF1ab/nsp31042K1042del1K1860del1delAaa-aa760.8571435843-5845
ORF1ab/nsp31042K1042del1K1860del1delAAA-GT710.1428575843-5845
ORF1ab/nsp31042K1042QK1860QnonsynAaaCaa2215843-5845
ORF1ab/nsp31042K1042XK1860XnonsynAaaTaa1115843-5845

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/nsp31042K1042EAaaGaa249249All0.000048
ORF1ab/nsp31042K1042EAaaGaa223223B.1.1.70.0002
ORF1ab/nsp31042K1042KaaAaaG206206All0.000039
ORF1ab/nsp31042K1042NaaAaaT130191All0.000025
ORF1ab/nsp31042K1042NaaAaaC61191All0.000012
ORF1ab/nsp31042K1042RaAaaGa9595All0.000018
ORF1ab/nsp31042K1042KaaAaaG6464B.1.1.70.000057
ORF1ab/nsp31042K1042TaAaaCa5959All0.000011
ORF1ab/nsp31042K1042TaAaaCa5252B.1.3480.945455
ORF1ab/nsp31042K1042NaaAaaT3336AY.430.000146
ORF1ab/nsp31042K1042NaaAaaC336AY.430.000013
ORF1ab/nsp31042K1042RaAaaGa3434B.1.1.2980.02931
ORF1ab/nsp31042K1042KaaAaaG3131B.1.10.000562
ORF1ab/nsp31042K1042NaaAaaC2828AY.4.2.10.004172
ORF1ab/nsp31042K1042KaaAaaG2222AY.40.000034
ORF1ab/nsp31042K1042KaaAaaG1919B.1.20.000167
ORF1ab/nsp31042K1042delAAA---1616All0.000003
ORF1ab/nsp31042K1042NaaAaaT1515B.1.10.000272
ORF1ab/nsp31042K1042IaAaaTa1414All0.000003
ORF1ab/nsp31042K1042NaaAaaT913B.1.1.70.000008
ORF1ab/nsp31042K1042NaaAaaC413B.1.1.70.000004
ORF1ab/nsp31042K1042IaAaaTa1111B.1.1.70.00001
ORF1ab/nsp31042K1042KaaAaaG1111B.1.1770.000145
ORF1ab/nsp31042K1042NaaAaaC59AY.340.000485
ORF1ab/nsp31042K1042NaaAaaT49AY.340.000388
ORF1ab/nsp31042K1042NaaAaaC89B.1.1.5190.000318
ORF1ab/nsp31042K1042NaaAaaT19B.1.1.5190.00004
ORF1ab/nsp31042K1042del1Aaa-aa67All0.000001
ORF1ab/nsp31042K1042del1AAA-GT17All0
ORF1ab/nsp31042K1042NaaAaaT77AY.460.000729
ORF1ab/nsp31042K1042RaAaaGa77B.1.1.70.000006
ORF1ab/nsp31042K1042KaaAaaG66AY.1030.000037
ORF1ab/nsp31042K1042NaaAaaC46AY.390.000099
ORF1ab/nsp31042K1042NaaAaaT26AY.390.000049
ORF1ab/nsp31042K1042NaaAaaT66AY.420.000241
ORF1ab/nsp31042K1042NaaAaaT66B0.000767
ORF1ab/nsp31042K1042KaaAaaG66B.1.617.20.000023
ORF1ab/nsp31042K1042RaAaaGa66B.1.6370.000438
ORF1ab/nsp31042K1042KaaAaaG66P.10.000095
ORF1ab/nsp31042K1042EAaaGaa55AY.1030.000031
ORF1ab/nsp31042K1042RaAaaGa55AY.230.000349
ORF1ab/nsp31042K1042RaAaaGa55AY.30.00005
ORF1ab/nsp31042K1042RaAaaGa55AY.410.00147
ORF1ab/nsp31042K1042NaaAaaT55C.36.30.002836
ORF1ab/nsp31042K1042NaaAaaT44AY.610.000419
ORF1ab/nsp31042K1042KaaAaaG44B.10.000037
ORF1ab/nsp31042K1042delAAA---44B.1.1.70.000004
ORF1ab/nsp31042K1042RaAaaGa44B.1.177.860.000734
ORF1ab/nsp31042K1042RaAaaGa44B.1.20.000035
ORF1ab/nsp31042K1042EAaaGaa44B.1.617.20.000015
ORF1ab/nsp31042K1042NaaAaaT34B.1.617.20.000011
ORF1ab/nsp31042K1042NaaAaaC14B.1.617.20.000004
ORF1ab/nsp31042K1042RaAaaGa33AY.1030.000019
ORF1ab/nsp31042K1042KaaAaaG33AY.1130.000427
ORF1ab/nsp31042K1042EAaaGaa33AY.1200.000112
ORF1ab/nsp31042K1042EAaaGaa33AY.40.000005
ORF1ab/nsp31042K1042RaAaaGa33AY.4.20.000065
ORF1ab/nsp31042K1042EAaaGaa33AY.430.000013
ORF1ab/nsp31042K1042NaaAaaT33AY.5.40.00083
ORF1ab/nsp31042K1042NaaAaaT33AY.9.10.000251
ORF1ab/nsp31042K1042NaaAaaT33AY.98.10.000145
ORF1ab/nsp31042K1042KaaAaaG33B.1.5260.000071
ORF1ab/nsp31042K1042KaaAaaG33D.20.000225
ORF1ab/nsp31042K1042QAaaCaa22All0
ORF1ab/nsp31042K1042KaaAaaG22AY.1180.000125
ORF1ab/nsp31042K1042TaAaaCa22AY.250.000012
ORF1ab/nsp31042K1042KaaAaaG22AY.250.000012
ORF1ab/nsp31042K1042RaAaaGa22AY.40.000003
ORF1ab/nsp31042K1042NaaAaaC22AY.40.000003
ORF1ab/nsp31042K1042KaaAaaG22AY.440.000012
ORF1ab/nsp31042K1042NaaAaaT22AY.620.000871
ORF1ab/nsp31042K1042NaaAaaT22AY.670.000929
ORF1ab/nsp31042K1042NaaAaaT22AY.7.20.001119
ORF1ab/nsp31042K1042NaaAaaT22B.10.000018
ORF1ab/nsp31042K1042TaAaaCa22B.10.000018
ORF1ab/nsp31042K1042EAaaGaa22B.10.000018
ORF1ab/nsp31042K1042del1AAA-GT12B.1.20.000009
ORF1ab/nsp31042K1042del1Aaa-aa12B.1.20.000009
ORF1ab/nsp31042K1042delAAA---22B.1.360.000292
ORF1ab/nsp31042K1042RaAaaGa22B.60.00182
ORF1ab/nsp31042K1042NaaAaaC12P.10.000016
ORF1ab/nsp31042K1042NaaAaaT12P.10.000016
ORF1ab/nsp31042K1042XAaaTaa11All0
ORF1ab/nsp31042K1042KaaAaaG11AY.1060.000335
ORF1ab/nsp31042K1042NaaAaaC11AY.1080.001103
ORF1ab/nsp31042K1042KaaAaaG11AY.1170.000085
ORF1ab/nsp31042K1042RaAaaGa11AY.1180.000063
ORF1ab/nsp31042K1042del1Aaa-aa11AY.1190.000035
ORF1ab/nsp31042K1042NaaAaaT11AY.1200.000037
ORF1ab/nsp31042K1042del1Aaa-aa11AY.1200.000037
ORF1ab/nsp31042K1042KaaAaaG11AY.200.000039
ORF1ab/nsp31042K1042EAaaGaa11AY.230.00007
ORF1ab/nsp31042K1042NaaAaaC11AY.250.000006
ORF1ab/nsp31042K1042EAaaGaa11AY.250.000006
ORF1ab/nsp31042K1042RaAaaGa11AY.250.000006
ORF1ab/nsp31042K1042del1Aaa-aa11AY.260.000028
ORF1ab/nsp31042K1042NaaAaaT11AY.260.000028
ORF1ab/nsp31042K1042KaaAaaG11AY.30.00001
ORF1ab/nsp31042K1042IaAaaTa11AY.30.00001
ORF1ab/nsp31042K1042delAAA---11AY.360.000148
ORF1ab/nsp31042K1042IaAaaTa11AY.40.000002
ORF1ab/nsp31042K1042delAAA---11AY.4.30.000842
ORF1ab/nsp31042K1042NaaAaaT11AY.4.50.000107
ORF1ab/nsp31042K1042delAAA---11AY.420.00004
ORF1ab/nsp31042K1042NaaAaaC11AY.440.000006
ORF1ab/nsp31042K1042EAaaGaa11AY.440.000006
ORF1ab/nsp31042K1042KaaAaaG11AY.46.40.000165
ORF1ab/nsp31042K1042KaaAaaG11AY.470.000031
ORF1ab/nsp31042K1042KaaAaaG11AY.480.000465
ORF1ab/nsp31042K1042IaAaaTa11AY.530.000288
ORF1ab/nsp31042K1042KaaAaaG11AY.580.000907
ORF1ab/nsp31042K1042NaaAaaT11AY.680.000274
ORF1ab/nsp31042K1042NaaAaaT11AY.700.000209
ORF1ab/nsp31042K1042delAAA---11AY.710.000475
ORF1ab/nsp31042K1042delAAA---11AY.850.000427
ORF1ab/nsp31042K1042RaAaaGa11AY.9.10.000084
ORF1ab/nsp31042K1042KaaAaaG11AY.9.20.000037
ORF1ab/nsp31042K1042del1Aaa-aa11AY.9.20.000037
ORF1ab/nsp31042K1042NaaAaaT11AY.980.000079
ORF1ab/nsp31042K1042TaAaaCa11B0.000128
ORF1ab/nsp31042K1042KaaAaaG11B0.000128
ORF1ab/nsp31042K1042RaAaaGa11B.10.000009
ORF1ab/nsp31042K1042RaAaaGa11B.1.10.000018
ORF1ab/nsp31042K1042NaaAaaT11B.1.1.100.001115
ORF1ab/nsp31042K1042delAAA---11B.1.1.1390.022727
ORF1ab/nsp31042K1042NaaAaaT11B.1.1.1610.003534
ORF1ab/nsp31042K1042RaAaaGa11B.1.1.1610.003534
ORF1ab/nsp31042K1042EAaaGaa11B.1.1.3170.000412
ORF1ab/nsp31042K1042KaaAaaG11B.1.1.3720.000689
ORF1ab/nsp31042K1042NaaAaaT11B.1.1.5120.028571
ORF1ab/nsp31042K1042KaaAaaG11B.1.1.5190.00004
ORF1ab/nsp31042K1042delAAA---11B.1.1.630.000386
ORF1ab/nsp31042K1042NaaAaaT11B.1.1600.000031
ORF1ab/nsp31042K1042KaaAaaG11B.1.1600.000031
ORF1ab/nsp31042K1042KaaAaaG11B.1.160.140.002119
ORF1ab/nsp31042K1042KaaAaaG11B.1.160.160.000929
ORF1ab/nsp31042K1042RaAaaGa11B.1.1770.000013
ORF1ab/nsp31042K1042QAaaCaa11B.1.1770.000013
ORF1ab/nsp31042K1042EAaaGaa11B.1.1770.000013
ORF1ab/nsp31042K1042RaAaaGa11B.1.177.160.000664
ORF1ab/nsp31042K1042NaaAaaT11B.1.177.750.001041
ORF1ab/nsp31042K1042NaaAaaT11B.1.177.830.001481
ORF1ab/nsp31042K1042KaaAaaG11B.1.177.850.005435
ORF1ab/nsp31042K1042TaAaaCa11B.1.20.000009
ORF1ab/nsp31042K1042NaaAaaT11B.1.20.000009
ORF1ab/nsp31042K1042KaaAaaG11B.1.2210.000071
ORF1ab/nsp31042K1042NaaAaaC11B.1.2430.00007
ORF1ab/nsp31042K1042delAAA---11B.1.2580.000067
ORF1ab/nsp31042K1042NaaAaaT11B.1.258.140.00098
ORF1ab/nsp31042K1042NaaAaaT11B.1.3490.000715
ORF1ab/nsp31042K1042KaaAaaG11B.1.3510.00003
ORF1ab/nsp31042K1042RaAaaGa11B.1.360.000146
ORF1ab/nsp31042K1042RaAaaGa11B.1.4040.001302
ORF1ab/nsp31042K1042NaaAaaT11B.1.4290.000024
ORF1ab/nsp31042K1042NaaAaaC11B.1.4970.000315
ORF1ab/nsp31042K1042RaAaaGa11B.1.5170.000427
ORF1ab/nsp31042K1042RaAaaGa11B.1.5960.000087
ORF1ab/nsp31042K1042KaaAaaG11B.1.5960.000087
ORF1ab/nsp31042K1042del1Aaa-aa11B.1.617.20.000004
ORF1ab/nsp31042K1042RaAaaGa11B.1.617.20.000004
ORF1ab/nsp31042K1042QAaaCaa11B.1.617.20.000004
ORF1ab/nsp31042K1042delAAA---11B.1.617.20.000004
ORF1ab/nsp31042K1042TaAaaCa11B.1.617.20.000004
ORF1ab/nsp31042K1042RaAaaGa11B.1.6210.000089
ORF1ab/nsp31042K1042delAAA---11B.150.017544
ORF1ab/nsp31042K1042XAaaTaa11C.350.000774
ORF1ab/nsp31042K1042EAaaGaa11C.350.000774
ORF1ab/nsp31042K1042KaaAaaG11C.350.000774
ORF1ab/nsp31042K1042KaaAaaG11C.370.000116
ORF1ab/nsp31042K1042NaaAaaT11P.1.10.000318
ORF1ab/nsp31042K1042RaAaaGa11P.1.100.000269
ORF1ab/nsp31042K1042KaaAaaG11P.1.150.000232

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.