CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp6 : CodonNum = 4

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/nsp64K4RK3573RnonsynaAaaGa707370720.99985910982-10984
ORF1ab/nsp64K4RK3573RnonsynaAAaGG707310.00014138310982-10984
ORF1ab/nsp64K4EK3573EnonsynAaaGaa10451045110982-10984
ORF1ab/nsp64K4KK3573KsynaaAaaG140140110982-10984
ORF1ab/nsp64K4QK3573QnonsynAaaCaa4949110982-10984
ORF1ab/nsp64K4delK3573deldelAAA---4242110982-10984
ORF1ab/nsp64K4NK3573NnonsynaaAaaC26180.69230810982-10984
ORF1ab/nsp64K4NK3573NnonsynaaAaaT2680.30769210982-10984
ORF1ab/nsp64K4IK3573InonsynaAaaTa21140.66666710982-10984
ORF1ab/nsp64K4IK3573InonsynaAAaTC2170.33333310982-10984
ORF1ab/nsp64K4TK3573TnonsynaAaaCa20190.9510982-10984
ORF1ab/nsp64K4TK3573TnonsynaAAaCC2010.0510982-10984
ORF1ab/nsp64K4LK3573LnonsynAAaTTa1170.63636410982-10984
ORF1ab/nsp64K4LK3573LnonsynAAACTC1120.18181810982-10984
ORF1ab/nsp64K4LK3573LnonsynAAACTT1120.18181810982-10984
ORF1ab/nsp64K4FK3573FnonsynAAATTC1090.910982-10984
ORF1ab/nsp64K4FK3573FnonsynAAATTT1010.110982-10984
ORF1ab/nsp64K4YK3573YnonsynAaATaC88110982-10984
ORF1ab/nsp64K4XK3573XnonsynAaaTaa88110982-10984
ORF1ab/nsp64K4del1K3573del1delAaa-aa77110982-10984
ORF1ab/nsp64K4GK3573GnonsynAAaGGa420.510982-10984
ORF1ab/nsp64K4GK3573GnonsynAAAGGG410.2510982-10984
ORF1ab/nsp64K4GK3573GnonsynAAAGGT410.2510982-10984
ORF1ab/nsp64K4del2K3573del2delAAa--a210.510982-10984
ORF1ab/nsp64K4del2K3573del2delaAAa--210.510982-10984
ORF1ab/nsp64K4DK3573DnonsynAaAGaT11110982-10984
ORF1ab/nsp64K4SK3573SnonsynaAAaGT11110982-10984
ORF1ab/nsp64K4VK3573VnonsynAAaGTa11110982-10984
ORF1ab/nsp64K4AK3573AnonsynAAaGCa11110982-10984

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/nsp64K4RaAaaGa70727073All0.001353
ORF1ab/nsp64K4RaAAaGG17073All0
ORF1ab/nsp64K4RaAaaGa66806680P.10.105237
ORF1ab/nsp64K4EAaaGaa10451045All0.0002
ORF1ab/nsp64K4EAaaGaa468468B.1.6270.945455
ORF1ab/nsp64K4EAaaGaa292292B.1.6310.983165
ORF1ab/nsp64K4KaaAaaG140140All0.000027
ORF1ab/nsp64K4RaAaaGa124124P.1.120.060019
ORF1ab/nsp64K4EAaaGaa102102AY.40.000159
ORF1ab/nsp64K4RaAaaGa5252P.1.150.012082
ORF1ab/nsp64K4QAaaCaa4949All0.000009
ORF1ab/nsp64K4EAaaGaa4949B.471
ORF1ab/nsp64K4RaAaaGa4444B.1.1.70.000039
ORF1ab/nsp64K4delAAA---4242All0.000008
ORF1ab/nsp64K4KaaAaaG3939B.1.1.70.000035
ORF1ab/nsp64K4EAaaGaa3636C.401
ORF1ab/nsp64K4KaaAaaG3333AY.1070.015377
ORF1ab/nsp64K4NaaAaaC1826All0.000003
ORF1ab/nsp64K4NaaAaaT826All0.000002
ORF1ab/nsp64K4IaAaaTa1421All0.000003
ORF1ab/nsp64K4IaAAaTC721All0.000001
ORF1ab/nsp64K4RaAaaGa2121B.1.1770.000277
ORF1ab/nsp64K4TaAaaCa1920All0.000004
ORF1ab/nsp64K4TaAAaCC120All0
ORF1ab/nsp64K4RaAaaGa1919P.1.10.006036
ORF1ab/nsp64K4EAaaGaa1717B.10.000156
ORF1ab/nsp64K4RaAaaGa1616B.1.177.820.007637
ORF1ab/nsp64K4RaAaaGa1414B.10.000128
ORF1ab/nsp64K4QAaaCaa1414B.1.2430.000974
ORF1ab/nsp64K4RaAaaGa1313AY.40.00002
ORF1ab/nsp64K4delAAA---1313B.1.1.70.000012
ORF1ab/nsp64K4LAAaTTa711All0.000001
ORF1ab/nsp64K4LAAACTT211All0
ORF1ab/nsp64K4LAAACTC211All0
ORF1ab/nsp64K4FAAATTC910All0.000002
ORF1ab/nsp64K4FAAATTT110All0
ORF1ab/nsp64K4RaAaaGa1010B.1.10.000181
ORF1ab/nsp64K4KaaAaaG99B.1.617.20.000034
ORF1ab/nsp64K4YAaATaC88All0.000002
ORF1ab/nsp64K4XAaaTaa88All0.000002
ORF1ab/nsp64K4EAaaGaa88B.1.1.3540.035088
ORF1ab/nsp64K4KaaAaaG88P.1.70.002554
ORF1ab/nsp64K4del1Aaa-aa77All0.000001
ORF1ab/nsp64K4QAaaCaa77AY.1030.000043
ORF1ab/nsp64K4RaAaaGa77AY.440.000043
ORF1ab/nsp64K4KaaAaaG77B.1.4290.000165
ORF1ab/nsp64K4RaAaaGa77P.1.10.10.056911
ORF1ab/nsp64K4RaAaaGa77P.1.160.002619
ORF1ab/nsp64K4EAaaGaa66B.1.1770.000079
ORF1ab/nsp64K4NaaAaaC56B.1.20.000044
ORF1ab/nsp64K4NaaAaaT16B.1.20.000009
ORF1ab/nsp64K4KaaAaaG66B.1.2790.003082
ORF1ab/nsp64K4EAaaGaa66B.1.617.20.000023
ORF1ab/nsp64K4IaAaaTa36P.10.000047
ORF1ab/nsp64K4IaAAaTC36P.10.000047
ORF1ab/nsp64K4delAAA---55AY.40.000008
ORF1ab/nsp64K4QAaaCaa55B.1.20.000044
ORF1ab/nsp64K4EAaaGaa55P.50.068493
ORF1ab/nsp64K4delAAA---440.222222
ORF1ab/nsp64K4GAAaGGa24All0
ORF1ab/nsp64K4GAAAGGG14All0
ORF1ab/nsp64K4GAAAGGT14All0
ORF1ab/nsp64K4EAaaGaa44B.1.10.000073
ORF1ab/nsp64K4RaAaaGa44B.1.1.2140.000222
ORF1ab/nsp64K4EAaaGaa44B.1.360.000584
ORF1ab/nsp64K4RaAaaGa44B.1.617.20.000015
ORF1ab/nsp64K4EAaaGaa44B.6.40.181818
ORF1ab/nsp64K4FAAATTC44P.10.000063
ORF1ab/nsp64K4IaAAaTC24P.1.120.000968
ORF1ab/nsp64K4IaAaaTa24P.1.120.000968
ORF1ab/nsp64K4RaAaaGa44P.1.140.000191
ORF1ab/nsp64K4IaAAaTC24P.20.000373
ORF1ab/nsp64K4IaAaaTa24P.20.000373
ORF1ab/nsp64K4IaAaaTa33AY.40.000005
ORF1ab/nsp64K4QAaaCaa33AY.430.000013
ORF1ab/nsp64K4EAaaGaa33AY.440.000018
ORF1ab/nsp64K4KaaAaaG33B.1.10.000054
ORF1ab/nsp64K4EAaaGaa33B.1.1.250.001706
ORF1ab/nsp64K4RaAaaGa33B.1.1.280.000934
ORF1ab/nsp64K4EAaaGaa33B.1.1.4120.022901
ORF1ab/nsp64K4RaAaaGa33B.1.1.5070.026087
ORF1ab/nsp64K4RaAaaGa33B.1.1.5280.014423
ORF1ab/nsp64K4NaaAaaC33B.1.1.70.000003
ORF1ab/nsp64K4TaAaaCa33B.1.617.20.000011
ORF1ab/nsp64K4KaaAaaG33B.1.6280.001057
ORF1ab/nsp64K4RaAaaGa33C.370.000348
ORF1ab/nsp64K4EAaaGaa33D.20.000225
ORF1ab/nsp64K4NaaAaaC33P.10.000047
ORF1ab/nsp64K4XAaaTaa33P.10.000047
ORF1ab/nsp64K4LAAaTTa33P.10.000047
ORF1ab/nsp64K4YAaATaC33P.10.000047
ORF1ab/nsp64K4RaAaaGa33P.1.130.002695
ORF1ab/nsp64K4EAaaGaa220.111111
ORF1ab/nsp64K4KaaAaaG220.111111
ORF1ab/nsp64K4GAAaGGa120.055556
ORF1ab/nsp64K4GAAAGGT120.055556
ORF1ab/nsp64K4QAaaCaa22A0.000774
ORF1ab/nsp64K4del2aAAa--12All0
ORF1ab/nsp64K4del2AAa--a12All0
ORF1ab/nsp64K4KaaAaaG22AY.1030.000012
ORF1ab/nsp64K4EAaaGaa22AY.200.000078
ORF1ab/nsp64K4RaAaaGa22AY.250.000012
ORF1ab/nsp64K4delAAA---22AY.290.000032
ORF1ab/nsp64K4RaAAaGG12AY.320.000532
ORF1ab/nsp64K4RaAaaGa12AY.320.000532
ORF1ab/nsp64K4KaaAaaG22AY.40.000003
ORF1ab/nsp64K4QAaaCaa22AY.40.000003
ORF1ab/nsp64K4NaaAaaT12AY.40.000002
ORF1ab/nsp64K4NaaAaaC12AY.40.000002
ORF1ab/nsp64K4RaAaaGa22AY.4.20.000043
ORF1ab/nsp64K4KaaAaaG22AY.460.000208
ORF1ab/nsp64K4KaaAaaG22AY.50.000041
ORF1ab/nsp64K4FAAATTT12AY.790.001211
ORF1ab/nsp64K4FAAATTC12AY.790.001211
ORF1ab/nsp64K4LAAACTC12AY.790.001211
ORF1ab/nsp64K4LAAACTT12AY.790.001211
ORF1ab/nsp64K4TaAaaCa22AY.840.000875
ORF1ab/nsp64K4QAaaCaa22B.10.000018
ORF1ab/nsp64K4TaAaaCa22B.10.000018
ORF1ab/nsp64K4KaaAaaG22B.10.000018
ORF1ab/nsp64K4QAaaCaa22B.1.10.000036
ORF1ab/nsp64K4delAAA---22B.1.10.000036
ORF1ab/nsp64K4QAaaCaa22B.1.1.2910.001485
ORF1ab/nsp64K4QAaaCaa22B.1.1.3170.000823
ORF1ab/nsp64K4KaaAaaG22B.1.1.370.000386
ORF1ab/nsp64K4EAaaGaa22B.1.3690.00057
ORF1ab/nsp64K4RaAaaGa22D.20.00015
ORF1ab/nsp64K4KaaAaaG22P.10.000032
ORF1ab/nsp64K4YAaATaC22P.1.120.000968
ORF1ab/nsp64K4LAAaTTa22P.1.120.000968
ORF1ab/nsp64K4XAaaTaa22P.1.120.000968
ORF1ab/nsp64K4NaaAaaC22P.1.120.000968
ORF1ab/nsp64K4FAAATTC22P.1.120.000968
ORF1ab/nsp64K4YAaATaC22P.20.000373
ORF1ab/nsp64K4NaaAaaC22P.20.000373
ORF1ab/nsp64K4RaAaaGa22P.20.000373
ORF1ab/nsp64K4LAAaTTa22P.20.000373
ORF1ab/nsp64K4XAaaTaa22P.20.000373
ORF1ab/nsp64K4FAAATTC22P.20.000373
ORF1ab/nsp64K4RaAaaGa22R.10.00018
ORF1ab/nsp64K4RaAaaGa110.055556
ORF1ab/nsp64K4SaAAaGT110.055556
ORF1ab/nsp64K4DAaAGaT110.055556
ORF1ab/nsp64K4TaAaaCa110.055556
ORF1ab/nsp64K4VAAaGTa110.055556
ORF1ab/nsp64K4AAAaGCa110.055556
ORF1ab/nsp64K4IaAaaTa110.055556
ORF1ab/nsp64K4NaaAaaT110.055556
ORF1ab/nsp64K4GAAaGGa11A0.000387
ORF1ab/nsp64K4RaAaaGa11A.2.50.000499
ORF1ab/nsp64K4SaAAaGT11All0
ORF1ab/nsp64K4DAaAGaT11All0
ORF1ab/nsp64K4VAAaGTa11All0
ORF1ab/nsp64K4AAAaGCa11All0
ORF1ab/nsp64K4NaaAaaT11AY.1030.000006
ORF1ab/nsp64K4TaAaaCa11AY.1030.000006
ORF1ab/nsp64K4RaAaaGa11AY.1190.000035
ORF1ab/nsp64K4EAaaGaa11AY.230.00007
ORF1ab/nsp64K4KaaAaaG11AY.23.10.000417
ORF1ab/nsp64K4TaAaaCa11AY.250.000006
ORF1ab/nsp64K4KaaAaaG11AY.250.000006
ORF1ab/nsp64K4EAaaGaa11AY.250.000006
ORF1ab/nsp64K4delAAA---11AY.250.000006
ORF1ab/nsp64K4NaaAaaC11AY.260.000028
ORF1ab/nsp64K4KaaAaaG11AY.260.000028
ORF1ab/nsp64K4KaaAaaG11AY.29.10.000221
ORF1ab/nsp64K4RaAaaGa11AY.3.10.000085
ORF1ab/nsp64K4KaaAaaG11AY.320.000532
ORF1ab/nsp64K4TaAaaCa11AY.390.000025
ORF1ab/nsp64K4del2AAa--a11AY.40.000002
ORF1ab/nsp64K4del1Aaa-aa11AY.40.000002
ORF1ab/nsp64K4TaAaaCa11AY.40.000002
ORF1ab/nsp64K4RaAaaGa11AY.4.10.000737
ORF1ab/nsp64K4NaaAaaT11AY.4.20.000022
ORF1ab/nsp64K4QAaaCaa11AY.4.20.000022
ORF1ab/nsp64K4EAaaGaa11AY.4.20.000022
ORF1ab/nsp64K4KaaAaaG11AY.4.50.000107
ORF1ab/nsp64K4delAAA---11AY.4.50.000107
ORF1ab/nsp64K4TaAaaCa11AY.4.50.000107
ORF1ab/nsp64K4LAAACTC11AY.430.000004
ORF1ab/nsp64K4RaAaaGa11AY.430.000004
ORF1ab/nsp64K4delAAA---11AY.430.000004
ORF1ab/nsp64K4TaAaaCa11AY.430.000004
ORF1ab/nsp64K4delAAA---11AY.440.000006
ORF1ab/nsp64K4TaAaaCa11AY.440.000006
ORF1ab/nsp64K4KaaAaaG11AY.440.000006
ORF1ab/nsp64K4QAaaCaa11AY.450.000122
ORF1ab/nsp64K4EAaaGaa11AY.46.50.000198
ORF1ab/nsp64K4RaAaaGa11AY.46.60.000072
ORF1ab/nsp64K4QAaaCaa11AY.5.40.000277
ORF1ab/nsp64K4delAAA---11AY.540.000095
ORF1ab/nsp64K4delAAA---11AY.660.00107
ORF1ab/nsp64K4IaAaaTa11AY.750.000056
ORF1ab/nsp64K4EAaaGaa11AY.9.10.000084
ORF1ab/nsp64K4RaAaaGa11AY.920.000287
ORF1ab/nsp64K4del1Aaa-aa11B.10.000009
ORF1ab/nsp64K4NaaAaaT11B.10.000009
ORF1ab/nsp64K4TaAaaCa11B.1.10.000018
ORF1ab/nsp64K4EAaaGaa11B.1.1.10.000327
ORF1ab/nsp64K4EAaaGaa11B.1.1.1180.010204
ORF1ab/nsp64K4delAAA---11B.1.1.1590.004673
ORF1ab/nsp64K4KaaAaaG11B.1.1.1700.001247
ORF1ab/nsp64K4KaaAaaG11B.1.1.2860.002899
ORF1ab/nsp64K4del1Aaa-aa11B.1.1.3060.000438
ORF1ab/nsp64K4RaAaaGa11B.1.1.3120.001912
ORF1ab/nsp64K4del1Aaa-aa11B.1.1.370.000193
ORF1ab/nsp64K4EAaaGaa11B.1.1.370.000193
ORF1ab/nsp64K4del1Aaa-aa11B.1.1.4090.002833
ORF1ab/nsp64K4EAaaGaa11B.1.1.4320.001266
ORF1ab/nsp64K4QAaaCaa11B.1.1.500.000679
ORF1ab/nsp64K4TaAaaCa11B.1.1.5190.00004
ORF1ab/nsp64K4EAaaGaa11B.1.1.5260.003546
ORF1ab/nsp64K4XAaaTaa11B.1.1.70.000001
ORF1ab/nsp64K4YAaATaC11B.1.1.70.000001
ORF1ab/nsp64K4TaAAaCC11B.1.1.70.000001
ORF1ab/nsp64K4QAaaCaa11B.1.1.70.000001
ORF1ab/nsp64K4GAAAGGG11B.1.1.70.000001
ORF1ab/nsp64K4EAaaGaa11B.1.1.700.000341
ORF1ab/nsp64K4del2aAAa--11B.1.1130.015625
ORF1ab/nsp64K4delAAA---11B.1.1600.000031
ORF1ab/nsp64K4KaaAaaG11B.1.1600.000031
ORF1ab/nsp64K4NaaAaaT11B.1.1600.000031
ORF1ab/nsp64K4KaaAaaG11B.1.1770.000013
ORF1ab/nsp64K4delAAA---11B.1.1770.000013
ORF1ab/nsp64K4NaaAaaC11B.1.1770.000013
ORF1ab/nsp64K4delAAA---11B.1.177.150.000631
ORF1ab/nsp64K4delAAA---11B.1.177.40.000211
ORF1ab/nsp64K4TaAaaCa11B.1.177.620.001192
ORF1ab/nsp64K4delAAA---11B.1.177.630.002703
ORF1ab/nsp64K4RaAaaGa11B.1.177.70.000165
ORF1ab/nsp64K4EAaaGaa11B.1.177.730.000566
ORF1ab/nsp64K4delAAA---11B.1.177.90.001332
ORF1ab/nsp64K4EAaaGaa11B.1.20.000009
ORF1ab/nsp64K4del1Aaa-aa11B.1.2100.002132
ORF1ab/nsp64K4EAaaGaa11B.1.221.30.000833
ORF1ab/nsp64K4IaAaaTa11B.1.2320.000537
ORF1ab/nsp64K4RaAaaGa11B.1.2400.000216
ORF1ab/nsp64K4TaAaaCa11B.1.2580.000067
ORF1ab/nsp64K4EAaaGaa11B.1.3050.002151
ORF1ab/nsp64K4RaAaaGa11B.1.3110.000275
ORF1ab/nsp64K4EAaaGaa11B.1.3490.000715
ORF1ab/nsp64K4RaAaaGa11B.1.3490.000715
ORF1ab/nsp64K4NaaAaaT11B.1.351.20.000303
ORF1ab/nsp64K4QAaaCaa11B.1.360.000146
ORF1ab/nsp64K4EAaaGaa11B.1.36.20.010753
ORF1ab/nsp64K4RaAaaGa11B.1.4160.001269
ORF1ab/nsp64K4QAaaCaa11B.1.4270.00005
ORF1ab/nsp64K4EAaaGaa11B.1.4290.000024
ORF1ab/nsp64K4IaAaaTa11B.1.4290.000024
ORF1ab/nsp64K4EAaaGaa11B.1.466.20.000391
ORF1ab/nsp64K4EAaaGaa11B.1.5090.000866
ORF1ab/nsp64K4RaAaaGa11B.1.5250.000113
ORF1ab/nsp64K4KaaAaaG11B.1.5260.000024
ORF1ab/nsp64K4EAaaGaa11B.1.5510.00129
ORF1ab/nsp64K4KaaAaaG11B.1.5600.00463
ORF1ab/nsp64K4KaaAaaG11B.1.5760.000907
ORF1ab/nsp64K4RaAaaGa11B.1.5820.000491
ORF1ab/nsp64K4LAAACTT11B.1.617.20.000004
ORF1ab/nsp64K4delAAA---11B.1.617.20.000004
ORF1ab/nsp64K4QAaaCaa11B.1.617.20.000004
ORF1ab/nsp64K4EAaaGaa11B.1.6280.000352
ORF1ab/nsp64K4RaAaaGa11B.1.6370.000073
ORF1ab/nsp64K4KaaAaaG11B.1.6370.000073
ORF1ab/nsp64K4del1Aaa-aa11B.1.700.02439
ORF1ab/nsp64K4RaAaaGa11B.1.840.020833
ORF1ab/nsp64K4delAAA---11N.40.004255
ORF1ab/nsp64K4EAaaGaa11P.10.000016
ORF1ab/nsp64K4RaAaaGa11P.1.100.000269
ORF1ab/nsp64K4KaaAaaG11P.1.120.000484
ORF1ab/nsp64K4EAaaGaa11P.1.120.000484
ORF1ab/nsp64K4EAaaGaa11P.20.000187
ORF1ab/nsp64K4delAAA---11Q.10.000126
ORF1ab/nsp64K4RaAaaGa11Q.80.000165
ORF1ab/nsp64K4EAaaGaa11R.10.00009

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.