CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1512

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/nsp31512A1512SA2330SnonsynGcaTca2622600.9923667253-7255
ORF1ab/nsp31512A1512SA2330SnonsynGcATcG26210.003816797253-7255
ORF1ab/nsp31512A1512SA2330SnonsynGcATcC26210.003816797253-7255
ORF1ab/nsp31512A1512AA2330AsyngcAgcG1521080.7105267253-7255
ORF1ab/nsp31512A1512AA2330AsyngcAgcT152310.2039477253-7255
ORF1ab/nsp31512A1512AA2330AsyngcAgcC152130.08552637253-7255
ORF1ab/nsp31512A1512delA2330deldelGCA---777717253-7255
ORF1ab/nsp31512A1512EA2330EnonsyngCagAa48470.9791677253-7255
ORF1ab/nsp31512A1512EA2330EnonsyngCAgAG4810.02083337253-7255
ORF1ab/nsp31512A1512GA2330GnonsyngCagGa25220.887253-7255
ORF1ab/nsp31512A1512GA2330GnonsyngCAgGC2520.087253-7255
ORF1ab/nsp31512A1512GA2330GnonsyngCAgGG2510.047253-7255
ORF1ab/nsp31512A1512VA2330VnonsyngCagTa24210.8757253-7255
ORF1ab/nsp31512A1512VA2330VnonsyngCAgTT2420.08333337253-7255
ORF1ab/nsp31512A1512VA2330VnonsyngCAgTC2410.04166677253-7255
ORF1ab/nsp31512A1512del1A2330del1delgcAgc-17140.8235297253-7255
ORF1ab/nsp31512A1512del1A2330del1delGca-ca1720.1176477253-7255
ORF1ab/nsp31512A1512del1A2330del1delGCA-TC1710.05882357253-7255
ORF1ab/nsp31512A1512TA2330TnonsynGcaAca121217253-7255
ORF1ab/nsp31512A1512RA2330RnonsynGCaAGa430.757253-7255
ORF1ab/nsp31512A1512RA2330RnonsynGCAAGG410.257253-7255
ORF1ab/nsp31512A1512PA2330PnonsynGcaCca3317253-7255
ORF1ab/nsp31512A1512XA2330XnonsynGCaTAa310.3333337253-7255
ORF1ab/nsp31512A1512XA2330XnonsynGCATAG310.3333337253-7255
ORF1ab/nsp31512A1512XA2330XnonsynGCaTGa310.3333337253-7255
ORF1ab/nsp31512A1512IA2330InonsynGCaATa2217253-7255
ORF1ab/nsp31512A1512MA2330MnonsynGCAATG2217253-7255
ORF1ab/nsp31512A1512LA2330LnonsynGCaTTa2217253-7255
ORF1ab/nsp31512A1512DA2330DnonsyngCAgAC1117253-7255
ORF1ab/nsp31512A1512QA2330QnonsynGCaCAa1117253-7255
ORF1ab/nsp31512A1512CA2330CnonsynGCATGC1117253-7255
ORF1ab/nsp31512A1512WA2330WnonsynGCATGG1117253-7255
ORF1ab/nsp31512A1512KA2330KnonsynGCaAAa1117253-7255
ORF1ab/nsp31512A1512YA2330YnonsynGCATAC1117253-7255

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/nsp31512A1512SGcaTca260262All0.00005
ORF1ab/nsp31512A1512SGcATcC1262All0
ORF1ab/nsp31512A1512SGcATcG1262All0
ORF1ab/nsp31512A1512AgcAgcG108152All0.000021
ORF1ab/nsp31512A1512AgcAgcT31152All0.000006
ORF1ab/nsp31512A1512AgcAgcC13152All0.000002
ORF1ab/nsp31512A1512SGcaTca108108AY.40.000168
ORF1ab/nsp31512A1512SGcaTca8989B.1.5910.946809
ORF1ab/nsp31512A1512delGCA---7777All0.000015
ORF1ab/nsp31512A1512EgCagAa4748All0.000009
ORF1ab/nsp31512A1512EgCAgAG148All0
ORF1ab/nsp31512A1512AgcAgcG1830B.1.1.70.000016
ORF1ab/nsp31512A1512AgcAgcT1030B.1.1.70.000009
ORF1ab/nsp31512A1512AgcAgcC230B.1.1.70.000002
ORF1ab/nsp31512A1512GgCagGa2225All0.000004
ORF1ab/nsp31512A1512GgCAgGC225All0
ORF1ab/nsp31512A1512GgCAgGG125All0
ORF1ab/nsp31512A1512VgCagTa2124All0.000004
ORF1ab/nsp31512A1512VgCAgTT224All0
ORF1ab/nsp31512A1512VgCAgTC124All0
ORF1ab/nsp31512A1512EgCagAa1919AY.40.00003
ORF1ab/nsp31512A1512AgcAgcG1318AY.40.00002
ORF1ab/nsp31512A1512AgcAgcT518AY.40.000008
ORF1ab/nsp31512A1512del1gcAgc-1417All0.000003
ORF1ab/nsp31512A1512del1Gca-ca217All0
ORF1ab/nsp31512A1512del1GCA-TC117All0
ORF1ab/nsp31512A1512delGCA---1717B.1.1.70.000015
ORF1ab/nsp31512A1512AgcAgcG1313AY.250.000078
ORF1ab/nsp31512A1512EgCagAa1313AY.4.50.001397
ORF1ab/nsp31512A1512SGcaTca1313B.1.617.20.000049
ORF1ab/nsp31512A1512TGcaAca1212All0.000002
ORF1ab/nsp31512A1512AgcAgcG1010B.1.5260.000235
ORF1ab/nsp31512A1512AgcAgcG48AY.1030.000025
ORF1ab/nsp31512A1512AgcAgcC38AY.1030.000019
ORF1ab/nsp31512A1512AgcAgcT18AY.1030.000006
ORF1ab/nsp31512A1512SGcaTca77B.10.000064
ORF1ab/nsp31512A1512delGCA---66B.1.617.20.000023
ORF1ab/nsp31512A1512SGcaTca55AY.1030.000031
ORF1ab/nsp31512A1512GgCagGa55AY.40.000008
ORF1ab/nsp31512A1512VgCagTa45B.10.000037
ORF1ab/nsp31512A1512AgcAgcT25B.10.000018
ORF1ab/nsp31512A1512AgcAgcG25B.10.000018
ORF1ab/nsp31512A1512AgcAgcC15B.10.000009
ORF1ab/nsp31512A1512VgCAgTC15B.10.000009
ORF1ab/nsp31512A1512AgcAgcG55B.1.20.000044
ORF1ab/nsp31512A1512delGCA---440.222222
ORF1ab/nsp31512A1512RGCaAGa34All0.000001
ORF1ab/nsp31512A1512RGCAAGG14All0
ORF1ab/nsp31512A1512AgcAgcG44AY.70.000784
ORF1ab/nsp31512A1512EgCagAa44AY.90.00027
ORF1ab/nsp31512A1512delGCA---44B.10.000037
ORF1ab/nsp31512A1512delGCA---44B.1.10.000073
ORF1ab/nsp31512A1512del1gcAgc-44B.1.20.000035
ORF1ab/nsp31512A1512SGcaTca130.055556
ORF1ab/nsp31512A1512XGCATAG130.055556
ORF1ab/nsp31512A1512XGCaTAa130.055556
ORF1ab/nsp31512A1512GgCAgGG130.055556
ORF1ab/nsp31512A1512GgCAgGC130.055556
ORF1ab/nsp31512A1512GgCagGa130.055556
ORF1ab/nsp31512A1512AgcAgcC130.055556
ORF1ab/nsp31512A1512AgcAgcG130.055556
ORF1ab/nsp31512A1512AgcAgcT130.055556
ORF1ab/nsp31512A1512SGcATcC130.055556
ORF1ab/nsp31512A1512SGcATcG130.055556
ORF1ab/nsp31512A1512XGCaTGa130.055556
ORF1ab/nsp31512A1512PGcaCca33All0.000001
ORF1ab/nsp31512A1512XGCaTGa13All0
ORF1ab/nsp31512A1512XGCaTAa13All0
ORF1ab/nsp31512A1512XGCATAG13All0
ORF1ab/nsp31512A1512AgcAgcT33AY.1000.000138
ORF1ab/nsp31512A1512GgCagGa33AY.4.50.000322
ORF1ab/nsp31512A1512SGcaTca33AY.440.000018
ORF1ab/nsp31512A1512EgCagAa33AY.80.001818
ORF1ab/nsp31512A1512AgcAgcG23AY.9.20.000073
ORF1ab/nsp31512A1512AgcAgcT13AY.9.20.000037
ORF1ab/nsp31512A1512delGCA---33B.1.1.2180.023077
ORF1ab/nsp31512A1512AgcAgcG33B.1.1.3060.001315
ORF1ab/nsp31512A1512VgCagTa33B.1.1.70.000003
ORF1ab/nsp31512A1512delGCA---33B.1.1770.00004
ORF1ab/nsp31512A1512delGCA---33B.1.4110.011111
ORF1ab/nsp31512A1512AgcAgcG33B.1.4500.034091
ORF1ab/nsp31512A1512LGCaTTa220.111111
ORF1ab/nsp31512A1512EgCAgAG120.055556
ORF1ab/nsp31512A1512EgCagAa120.055556
ORF1ab/nsp31512A1512VgCAgTT120.055556
ORF1ab/nsp31512A1512VgCagTa120.055556
ORF1ab/nsp31512A1512LGCaTTa22All0
ORF1ab/nsp31512A1512IGCaATa22All0
ORF1ab/nsp31512A1512MGCAATG22All0
ORF1ab/nsp31512A1512AgcAgcG22AY.200.000078
ORF1ab/nsp31512A1512del1gcAgc-22AY.250.000012
ORF1ab/nsp31512A1512AgcAgcT12AY.30.00001
ORF1ab/nsp31512A1512AgcAgcG12AY.30.00001
ORF1ab/nsp31512A1512AgcAgcT12AY.390.000025
ORF1ab/nsp31512A1512AgcAgcG12AY.390.000025
ORF1ab/nsp31512A1512delGCA---22AY.40.000003
ORF1ab/nsp31512A1512delGCA---22AY.420.00008
ORF1ab/nsp31512A1512SGcaTca22AY.420.00008
ORF1ab/nsp31512A1512delGCA---22AY.430.000009
ORF1ab/nsp31512A1512RGCaAGa12AY.440.000006
ORF1ab/nsp31512A1512RGCAAGG12AY.440.000006
ORF1ab/nsp31512A1512SGcaTca22AY.700.000417
ORF1ab/nsp31512A1512GgCagGa22AY.80.001212
ORF1ab/nsp31512A1512GgCagGa12B.10.000009
ORF1ab/nsp31512A1512del1GCA-TC12B.10.000009
ORF1ab/nsp31512A1512GgCAgGC12B.10.000009
ORF1ab/nsp31512A1512del1gcAgc-12B.10.000009
ORF1ab/nsp31512A1512SGcaTca22B.1.10.000036
ORF1ab/nsp31512A1512TGcaAca22B.1.1.70.000002
ORF1ab/nsp31512A1512GgCagGa22B.1.1770.000026
ORF1ab/nsp31512A1512AgcAgcG22B.1.1770.000026
ORF1ab/nsp31512A1512delGCA---22B.1.177.620.002384
ORF1ab/nsp31512A1512AgcAgcG22B.1.2400.000431
ORF1ab/nsp31512A1512AgcAgcT22B.1.36.380.003284
ORF1ab/nsp31512A1512SGcaTca22B.1.5950.000522
ORF1ab/nsp31512A1512AgcAgcG22B.1.617.20.000008
ORF1ab/nsp31512A1512GgCagGa22B.1.617.20.000008
ORF1ab/nsp31512A1512AgcAgcG22B.1.90.012346
ORF1ab/nsp31512A1512SGcaTca22P.10.000032
ORF1ab/nsp31512A1512GgCagGa22P.1.10.000635
ORF1ab/nsp31512A1512AgcAgcG22R.10.00018
ORF1ab/nsp31512A1512WGCATGG110.055556
ORF1ab/nsp31512A1512CGCATGC110.055556
ORF1ab/nsp31512A1512DgCAgAC110.055556
ORF1ab/nsp31512A1512YGCATAC110.055556
ORF1ab/nsp31512A1512VgCagTa11A.2.40.003367
ORF1ab/nsp31512A1512PGcaCca11A.2.40.003367
ORF1ab/nsp31512A1512QGCaCAa11A.2.40.003367
ORF1ab/nsp31512A1512EgCagAa11A.2.40.003367
ORF1ab/nsp31512A1512AgcAgcC11A.23.10.000704
ORF1ab/nsp31512A1512delGCA---11AD.20.000219
ORF1ab/nsp31512A1512DgCAgAC11All0
ORF1ab/nsp31512A1512KGCaAAa11All0
ORF1ab/nsp31512A1512WGCATGG11All0
ORF1ab/nsp31512A1512CGCATGC11All0
ORF1ab/nsp31512A1512QGCaCAa11All0
ORF1ab/nsp31512A1512YGCATAC11All0
ORF1ab/nsp31512A1512del1gcAgc-11AU.10.001266
ORF1ab/nsp31512A1512delGCA---11AY.1010.00049
ORF1ab/nsp31512A1512SGcaTca11AY.1020.000027
ORF1ab/nsp31512A1512GgCagGa11AY.1200.000037
ORF1ab/nsp31512A1512EgCagAa11AY.1200.000037
ORF1ab/nsp31512A1512delGCA---11AY.1200.000037
ORF1ab/nsp31512A1512TGcaAca11AY.130.000161
ORF1ab/nsp31512A1512EgCagAa11AY.170.008197
ORF1ab/nsp31512A1512SGcaTca11AY.200.000039
ORF1ab/nsp31512A1512delGCA---11AY.250.000006
ORF1ab/nsp31512A1512VgCagTa11AY.250.000006
ORF1ab/nsp31512A1512AgcAgcT11AY.260.000028
ORF1ab/nsp31512A1512SGcaTca11AY.30.00001
ORF1ab/nsp31512A1512del1Gca-ca11AY.30.00001
ORF1ab/nsp31512A1512EgCagAa11AY.300.000396
ORF1ab/nsp31512A1512SGcaTca11AY.300.000396
ORF1ab/nsp31512A1512AgcAgcG11AY.330.000067
ORF1ab/nsp31512A1512delGCA---11AY.360.000148
ORF1ab/nsp31512A1512SGcaTca11AY.390.000025
ORF1ab/nsp31512A1512del1gcAgc-11AY.390.000025
ORF1ab/nsp31512A1512VgCagTa11AY.40.000002
ORF1ab/nsp31512A1512TGcaAca11AY.40.000002
ORF1ab/nsp31512A1512PGcaCca11AY.40.000002
ORF1ab/nsp31512A1512delGCA---11AY.4.30.000842
ORF1ab/nsp31512A1512delGCA---11AY.4.50.000107
ORF1ab/nsp31512A1512VgCagTa11AY.420.00004
ORF1ab/nsp31512A1512del1gcAgc-11AY.420.00004
ORF1ab/nsp31512A1512TGcaAca11AY.430.000004
ORF1ab/nsp31512A1512AgcAgcG11AY.430.000004
ORF1ab/nsp31512A1512RGCaAGa11AY.430.000004
ORF1ab/nsp31512A1512SGcaTca11AY.430.000004
ORF1ab/nsp31512A1512del1gcAgc-11AY.430.000004
ORF1ab/nsp31512A1512IGCaATa11AY.440.000006
ORF1ab/nsp31512A1512MGCAATG11AY.440.000006
ORF1ab/nsp31512A1512VgCagTa11AY.440.000006
ORF1ab/nsp31512A1512AgcAgcG11AY.450.000122
ORF1ab/nsp31512A1512AgcAgcC11AY.460.000104
ORF1ab/nsp31512A1512SGcaTca11AY.46.60.000072
ORF1ab/nsp31512A1512SGcaTca11AY.50.000021
ORF1ab/nsp31512A1512delGCA---11AY.50.000021
ORF1ab/nsp31512A1512AgcAgcG11AY.60.000041
ORF1ab/nsp31512A1512delGCA---11AY.660.00107
ORF1ab/nsp31512A1512SGcaTca11AY.680.000274
ORF1ab/nsp31512A1512AgcAgcG11AY.690.000187
ORF1ab/nsp31512A1512del1gcAgc-11AY.750.000056
ORF1ab/nsp31512A1512delGCA---11AY.760.004831
ORF1ab/nsp31512A1512RGCaAGa11AY.840.000437
ORF1ab/nsp31512A1512TGcaAca11AY.90.000068
ORF1ab/nsp31512A1512SGcaTca11AY.90.000068
ORF1ab/nsp31512A1512GgCagGa11AY.90.000068
ORF1ab/nsp31512A1512SGcaTca11AY.9.10.000084
ORF1ab/nsp31512A1512MGCAATG11AY.9.20.000037
ORF1ab/nsp31512A1512AgcAgcG11AY.930.000273
ORF1ab/nsp31512A1512SGcaTca11AY.980.000079
ORF1ab/nsp31512A1512delGCA---11AY.990.001049
ORF1ab/nsp31512A1512TGcaAca11B.10.000009
ORF1ab/nsp31512A1512KGCaAAa11B.1.10.000018
ORF1ab/nsp31512A1512IGCaATa11B.1.10.000018
ORF1ab/nsp31512A1512VgCagTa11B.1.10.000018
ORF1ab/nsp31512A1512AgcAgcC11B.1.10.000018
ORF1ab/nsp31512A1512AgcAgcG11B.1.1.10.000327
ORF1ab/nsp31512A1512TGcaAca11B.1.1.100.001115
ORF1ab/nsp31512A1512AgcAgcT11B.1.1.2160.00089
ORF1ab/nsp31512A1512VgCagTa11B.1.1.2220.000204
ORF1ab/nsp31512A1512VgCagTa11B.1.1.2340.012048
ORF1ab/nsp31512A1512SGcaTca11B.1.1.370.000193
ORF1ab/nsp31512A1512delGCA---11B.1.1.370.000193
ORF1ab/nsp31512A1512TGcaAca11B.1.1.370.000193
ORF1ab/nsp31512A1512SGcaTca11B.1.1.390.00051
ORF1ab/nsp31512A1512delGCA---11B.1.1.460.004367
ORF1ab/nsp31512A1512delGCA---11B.1.1.4640.001473
ORF1ab/nsp31512A1512AgcAgcC11B.1.1.5190.00004
ORF1ab/nsp31512A1512delGCA---11B.1.1.5250.005464
ORF1ab/nsp31512A1512VgCagTa11B.1.1.570.011494
ORF1ab/nsp31512A1512EgCagAa11B.1.1.70.000001
ORF1ab/nsp31512A1512del1gcAgc-11B.1.1.70.000001
ORF1ab/nsp31512A1512EgCagAa11B.1.130.002375
ORF1ab/nsp31512A1512AgcAgcT11B.1.1600.000031
ORF1ab/nsp31512A1512TGcaAca11B.1.1770.000013
ORF1ab/nsp31512A1512SGcaTca11B.1.1770.000013
ORF1ab/nsp31512A1512VgCagTa11B.1.177.120.000152
ORF1ab/nsp31512A1512SGcaTca11B.1.177.50.001242
ORF1ab/nsp31512A1512SGcaTca11B.1.177.60.000977
ORF1ab/nsp31512A1512EgCagAa11B.1.20.000009
ORF1ab/nsp31512A1512SGcaTca11B.1.20.000009
ORF1ab/nsp31512A1512delGCA---11B.1.20.000009
ORF1ab/nsp31512A1512delGCA---11B.1.2100.002132
ORF1ab/nsp31512A1512AgcAgcC11B.1.2100.002132
ORF1ab/nsp31512A1512GgCagGa11B.1.2210.000071
ORF1ab/nsp31512A1512AgcAgcG11B.1.2430.00007
ORF1ab/nsp31512A1512del1gcAgc-11B.1.2430.00007
ORF1ab/nsp31512A1512AgcAgcG11B.1.258.170.000104
ORF1ab/nsp31512A1512SGcaTca11B.1.258.170.000104
ORF1ab/nsp31512A1512SGcaTca11B.1.3510.00003
ORF1ab/nsp31512A1512AgcAgcG11B.1.3510.00003
ORF1ab/nsp31512A1512delGCA---11B.1.3690.000285
ORF1ab/nsp31512A1512AgcAgcG11B.1.4000.000429
ORF1ab/nsp31512A1512delGCA---11B.1.416.10.001563
ORF1ab/nsp31512A1512AgcAgcG11B.1.4270.00005
ORF1ab/nsp31512A1512PGcaCca11B.1.4290.000024
ORF1ab/nsp31512A1512delGCA---11B.1.4530.003236
ORF1ab/nsp31512A1512delGCA---11B.1.5260.000024
ORF1ab/nsp31512A1512AgcAgcG11B.1.5450.014493
ORF1ab/nsp31512A1512VgCagTa11B.1.5600.00463
ORF1ab/nsp31512A1512delGCA---11B.1.5770.000687
ORF1ab/nsp31512A1512AgcAgcG11B.1.5770.000687
ORF1ab/nsp31512A1512SGcaTca11B.1.5800.004065
ORF1ab/nsp31512A1512delGCA---11B.1.617.10.000129
ORF1ab/nsp31512A1512TGcaAca11B.1.617.20.000004
ORF1ab/nsp31512A1512VgCagTa11B.1.617.20.000004
ORF1ab/nsp31512A1512GgCagGa11B.1.619.10.000641
ORF1ab/nsp31512A1512delGCA---11B.1.6210.000089
ORF1ab/nsp31512A1512AgcAgcC11B.1.6210.000089
ORF1ab/nsp31512A1512del1Gca-ca11B.1.6210.000089
ORF1ab/nsp31512A1512TGcaAca11B.1.6210.000089
ORF1ab/nsp31512A1512AgcAgcG11B.1.6280.000352
ORF1ab/nsp31512A1512VgCagTa11B.1.6370.000073
ORF1ab/nsp31512A1512VgCAgTT11C.350.000774
ORF1ab/nsp31512A1512SGcaTca11C.360.000911
ORF1ab/nsp31512A1512SGcaTca11C.36.30.000567
ORF1ab/nsp31512A1512SGcaTca11P.1.10.000318
ORF1ab/nsp31512A1512AgcAgcT11P.1.140.000048
ORF1ab/nsp31512A1512delGCA---11P.1.150.000232
ORF1ab/nsp31512A1512AgcAgcG11P.60.003145

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.