CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : Mut = A1878A

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/nsp31878A1878AA2696AsyngcGgcA201915000.7429428351-8353
ORF1ab/nsp31878A1878AA2696AsyngcGgcT20195110.2530968351-8353
ORF1ab/nsp31878A1878AA2696AsyngcGgcC201980.003962368351-8353

Details of the mutation A1878A within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF1ab/nsp31878A1878AgcGgcA15002019All0.000287
ORF1ab/nsp31878A1878AgcGgcT5112019All0.000098
ORF1ab/nsp31878A1878AgcGgcC82019All0.000002
ORF1ab/nsp31878A1878AgcGgcA576576C.300.994819
ORF1ab/nsp31878A1878AgcGgcA216336B.1.1.70.000193
ORF1ab/nsp31878A1878AgcGgcT119336B.1.1.70.000107
ORF1ab/nsp31878A1878AgcGgcC1336B.1.1.70.000001
ORF1ab/nsp31878A1878AgcGgcA149149C.30.11
ORF1ab/nsp31878A1878AgcGgcA123125B.1.1.10.040183
ORF1ab/nsp31878A1878AgcGgcT2125B.1.1.10.000653
ORF1ab/nsp31878A1878AgcGgcA96113B.1.20.000845
ORF1ab/nsp31878A1878AgcGgcT17113B.1.20.00015
ORF1ab/nsp31878A1878AgcGgcA4990AY.40.000076
ORF1ab/nsp31878A1878AgcGgcT4190AY.40.000064
ORF1ab/nsp31878A1878AgcGgcA4179B.1.617.20.000154
ORF1ab/nsp31878A1878AgcGgcT3879B.1.617.20.000143
ORF1ab/nsp31878A1878AgcGgcT6060B.1.5250.00679
ORF1ab/nsp31878A1878AgcGgcA5454C.310.964286
ORF1ab/nsp31878A1878AgcGgcA2027B.10.000183
ORF1ab/nsp31878A1878AgcGgcT727B.10.000064
ORF1ab/nsp31878A1878AgcGgcT2525B.1.1.280.007781
ORF1ab/nsp31878A1878AgcGgcT2125C.370.002437
ORF1ab/nsp31878A1878AgcGgcC425C.370.000464
ORF1ab/nsp31878A1878AgcGgcT1924AY.440.000116
ORF1ab/nsp31878A1878AgcGgcA524AY.440.00003
ORF1ab/nsp31878A1878AgcGgcT2023AY.30.000199
ORF1ab/nsp31878A1878AgcGgcA323AY.30.00003
ORF1ab/nsp31878A1878AgcGgcA1719B.1.1770.000224
ORF1ab/nsp31878A1878AgcGgcT219B.1.1770.000026
ORF1ab/nsp31878A1878AgcGgcA815AY.1020.000212
ORF1ab/nsp31878A1878AgcGgcT615AY.1020.000159
ORF1ab/nsp31878A1878AgcGgcC115AY.1020.000027
ORF1ab/nsp31878A1878AgcGgcT912AY.430.00004
ORF1ab/nsp31878A1878AgcGgcA312AY.430.000013
ORF1ab/nsp31878A1878AgcGgcA712B.1.10.000127
ORF1ab/nsp31878A1878AgcGgcT512B.1.10.000091
ORF1ab/nsp31878A1878AgcGgcA1212B.1.1260.015306
ORF1ab/nsp31878A1878AgcGgcA1212B.1.160.120.076923
ORF1ab/nsp31878A1878AgcGgcT712P.10.00011
ORF1ab/nsp31878A1878AgcGgcA512P.10.000079
ORF1ab/nsp31878A1878AgcGgcA99AY.750.000504
ORF1ab/nsp31878A1878AgcGgcT79B.1.4290.000165
ORF1ab/nsp31878A1878AgcGgcA29B.1.4290.000047
ORF1ab/nsp31878A1878AgcGgcA58AY.250.00003
ORF1ab/nsp31878A1878AgcGgcT38AY.250.000018
ORF1ab/nsp31878A1878AgcGgcA47AY.1030.000025
ORF1ab/nsp31878A1878AgcGgcT37AY.1030.000019
ORF1ab/nsp31878A1878AgcGgcT67AY.200.000233
ORF1ab/nsp31878A1878AgcGgcA17AY.200.000039
ORF1ab/nsp31878A1878AgcGgcA77AY.530.002013
ORF1ab/nsp31878A1878AgcGgcA45AY.90.00027
ORF1ab/nsp31878A1878AgcGgcT15AY.90.000068
ORF1ab/nsp31878A1878AgcGgcT55B.1.6200.00473
ORF1ab/nsp31878A1878AgcGgcT34AY.1000.000138
ORF1ab/nsp31878A1878AgcGgcA14AY.1000.000046
ORF1ab/nsp31878A1878AgcGgcT34AY.1210.000406
ORF1ab/nsp31878A1878AgcGgcA14AY.1210.000135
ORF1ab/nsp31878A1878AgcGgcT44AY.350.000932
ORF1ab/nsp31878A1878AgcGgcT44AY.4.20.000087
ORF1ab/nsp31878A1878AgcGgcA44AY.99.20.000369
ORF1ab/nsp31878A1878AgcGgcA44B.1.177.440.002076
ORF1ab/nsp31878A1878AgcGgcT44B.1.3510.000119
ORF1ab/nsp31878A1878AgcGgcA24B.1.5960.000174
ORF1ab/nsp31878A1878AgcGgcT24B.1.5960.000174
ORF1ab/nsp31878A1878AgcGgcA24B.1.617.10.000258
ORF1ab/nsp31878A1878AgcGgcT24B.1.617.10.000258
ORF1ab/nsp31878A1878AgcGgcA33AY.20.001068
ORF1ab/nsp31878A1878AgcGgcT33AY.360.000445
ORF1ab/nsp31878A1878AgcGgcA23AY.390.000049
ORF1ab/nsp31878A1878AgcGgcT13AY.390.000025
ORF1ab/nsp31878A1878AgcGgcT33AY.46.20.001906
ORF1ab/nsp31878A1878AgcGgcA33AY.470.000093
ORF1ab/nsp31878A1878AgcGgcA23AY.50.000041
ORF1ab/nsp31878A1878AgcGgcT13AY.50.000021
ORF1ab/nsp31878A1878AgcGgcT33B.1.1.3260.005282
ORF1ab/nsp31878A1878AgcGgcA23B.1.177.730.001133
ORF1ab/nsp31878A1878AgcGgcT13B.1.177.730.000566
ORF1ab/nsp31878A1878AgcGgcA23B.1.2580.000133
ORF1ab/nsp31878A1878AgcGgcT13B.1.2580.000067
ORF1ab/nsp31878A1878AgcGgcT23B.1.5260.000047
ORF1ab/nsp31878A1878AgcGgcA13B.1.5260.000024
ORF1ab/nsp31878A1878AgcGgcT33M.10.069767
ORF1ab/nsp31878A1878AgcGgcA33P.1.40.00293
ORF1ab/nsp31878A1878AgcGgcT220.111111
ORF1ab/nsp31878A1878AgcGgcT22AY.1170.000169
ORF1ab/nsp31878A1878AgcGgcA22AY.1180.000125
ORF1ab/nsp31878A1878AgcGgcT22AY.240.000862
ORF1ab/nsp31878A1878AgcGgcT12AY.260.000028
ORF1ab/nsp31878A1878AgcGgcA12AY.260.000028
ORF1ab/nsp31878A1878AgcGgcT22AY.480.00093
ORF1ab/nsp31878A1878AgcGgcA22AY.5.30.000675
ORF1ab/nsp31878A1878AgcGgcA22AY.620.000871
ORF1ab/nsp31878A1878AgcGgcT22AY.770.002255
ORF1ab/nsp31878A1878AgcGgcA22B0.000256
ORF1ab/nsp31878A1878AgcGgcA22B.1.1.1940.009901
ORF1ab/nsp31878A1878AgcGgcA22B.1.1.2140.000111
ORF1ab/nsp31878A1878AgcGgcT22B.1.1.3540.008772
ORF1ab/nsp31878A1878AgcGgcA12B.1.1.3890.006061
ORF1ab/nsp31878A1878AgcGgcT12B.1.1.3890.006061
ORF1ab/nsp31878A1878AgcGgcT22B.1.1.4320.002532
ORF1ab/nsp31878A1878AgcGgcT22B.1.177.210.000153
ORF1ab/nsp31878A1878AgcGgcT22B.1.177.820.000955
ORF1ab/nsp31878A1878AgcGgcT12B.1.2430.00007
ORF1ab/nsp31878A1878AgcGgcA12B.1.2430.00007
ORF1ab/nsp31878A1878AgcGgcA22B.1.466.20.000782
ORF1ab/nsp31878A1878AgcGgcT22B.1.4700.002809
ORF1ab/nsp31878A1878AgcGgcT22B.1.4970.00063
ORF1ab/nsp31878A1878AgcGgcA22P.1.140.000096
ORF1ab/nsp31878A1878AgcGgcA22Q.10.000253
ORF1ab/nsp31878A1878AgcGgcT11A.20.000662
ORF1ab/nsp31878A1878AgcGgcA11AN.10.02
ORF1ab/nsp31878A1878AgcGgcT11AY.1090.00074
ORF1ab/nsp31878A1878AgcGgcC11AY.1130.000142
ORF1ab/nsp31878A1878AgcGgcA11AY.120.000316
ORF1ab/nsp31878A1878AgcGgcT11AY.1200.000037
ORF1ab/nsp31878A1878AgcGgcA11AY.130.000161
ORF1ab/nsp31878A1878AgcGgcT11AY.140.000088
ORF1ab/nsp31878A1878AgcGgcA11AY.23.10.000417
ORF1ab/nsp31878A1878AgcGgcA11AY.290.000016
ORF1ab/nsp31878A1878AgcGgcT11AY.340.000097
ORF1ab/nsp31878A1878AgcGgcA11AY.39.10.00004
ORF1ab/nsp31878A1878AgcGgcT11AY.420.00004
ORF1ab/nsp31878A1878AgcGgcT11AY.450.000122
ORF1ab/nsp31878A1878AgcGgcA11AY.46.40.000165
ORF1ab/nsp31878A1878AgcGgcA11AY.5.40.000277
ORF1ab/nsp31878A1878AgcGgcT11AY.520.000814
ORF1ab/nsp31878A1878AgcGgcT11AY.540.000095
ORF1ab/nsp31878A1878AgcGgcT11AY.550.000917
ORF1ab/nsp31878A1878AgcGgcT11AY.590.00053
ORF1ab/nsp31878A1878AgcGgcA11AY.70.000196
ORF1ab/nsp31878A1878AgcGgcT11AY.7.20.000559
ORF1ab/nsp31878A1878AgcGgcT11AY.9.10.000084
ORF1ab/nsp31878A1878AgcGgcA11AY.980.000079
ORF1ab/nsp31878A1878AgcGgcT11AY.98.10.000048
ORF1ab/nsp31878A1878AgcGgcT11B.1.1.2840.000107
ORF1ab/nsp31878A1878AgcGgcA11B.1.1.3280.016949
ORF1ab/nsp31878A1878AgcGgcA11B.1.1.3480.000796
ORF1ab/nsp31878A1878AgcGgcA11B.1.1.3720.000689
ORF1ab/nsp31878A1878AgcGgcA11B.1.1.390.00051
ORF1ab/nsp31878A1878AgcGgcT11B.1.1.4670.019231
ORF1ab/nsp31878A1878AgcGgcC11B.1.1.5190.00004
ORF1ab/nsp31878A1878AgcGgcA11B.1.1.630.000386
ORF1ab/nsp31878A1878AgcGgcA11B.1.1600.000031
ORF1ab/nsp31878A1878AgcGgcA11B.1.177.860.000183
ORF1ab/nsp31878A1878AgcGgcT11B.1.351.20.000303
ORF1ab/nsp31878A1878AgcGgcT11B.1.360.000146
ORF1ab/nsp31878A1878AgcGgcA11B.1.4200.010417
ORF1ab/nsp31878A1878AgcGgcT11B.1.4740.001901
ORF1ab/nsp31878A1878AgcGgcT11B.1.617.30.002985
ORF1ab/nsp31878A1878AgcGgcA11B.1.6230.000536
ORF1ab/nsp31878A1878AgcGgcT11B.1.6280.000352
ORF1ab/nsp31878A1878AgcGgcT11B.550.00295
ORF1ab/nsp31878A1878AgcGgcT11C.37.10.002618

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.