CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF3a : CodonNum = 28

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
ORF3a28F28deldelTTT---20692069125474-25476
ORF3a28F28LnonsynttTttA7464640.62198425474-25476
ORF3a28F28LnonsynTttCtt7462560.34316425474-25476
ORF3a28F28LnonsynttTttG746230.030831125474-25476
ORF3a28F28LnonsynTtTCtC74620.0026809725474-25476
ORF3a28F28LnonsynTtTCtA74610.0013404825474-25476
ORF3a28F28SnonsyntTttCt267267125474-25476
ORF3a28F28FsynttTttC240240125474-25476
ORF3a28F28InonsynTttAtt4747125474-25476
ORF3a28F28del2delTTt--t45430.95555625474-25476
ORF3a28F28del2deltTTt--4510.022222225474-25476
ORF3a28F28del2delTTT--N4510.022222225474-25476
ORF3a28F28del1delTtt-tt36350.97222225474-25476
ORF3a28F28del1delTTt-Nt3610.027777825474-25476
ORF3a28F28VnonsynTttGtt33310.93939425474-25476
ORF3a28F28VnonsynTtTGtG3320.060606125474-25476
ORF3a28F28YnonsyntTttAt17150.88235325474-25476
ORF3a28F28YnonsyntTTtAC1720.11764725474-25476
ORF3a28F28CnonsyntTttGt1010125474-25476
ORF3a28F28GnonsynTTtGGt77125474-25476
ORF3a28F28HnonsynTTtCAt420.525474-25476
ORF3a28F28HnonsynTTTCAC420.525474-25476
ORF3a28F28PnonsynTTtCCt320.66666725474-25476
ORF3a28F28PnonsynTTTCCC310.33333325474-25476

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
ORF3a28F28delTTT---20692069All0.000396
ORF3a28F28delTTT---12331233B.1.214.20.739209
ORF3a28F28LttTttA464746All0.000089
ORF3a28F28LTttCtt256746All0.000049
ORF3a28F28LttTttG23746All0.000004
ORF3a28F28LTtTCtC2746All0
ORF3a28F28LTtTCtA1746All0
ORF3a28F28LttTttA274281B.1.10.004971
ORF3a28F28LTttCtt7281B.1.10.000127
ORF3a28F28StTttCt267267All0.000051
ORF3a28F28FttTttC240240All0.000046
ORF3a28F28delTTT---216216AY.490.690096
ORF3a28F28StTttCt207207B.1.1.70.000185
ORF3a28F28LTttCtt133157B.1.1.70.000119
ORF3a28F28LttTttG17157B.1.1.70.000015
ORF3a28F28LttTttA7157B.1.1.70.000006
ORF3a28F28delTTT---105105B.1.617.30.313433
ORF3a28F28FttTttC7171AY.39.10.002813
ORF3a28F28delTTT---5454AY.40.000084
ORF3a28F28LttTttA5454B.1.1.5220.931034
ORF3a28F28ITttAtt4747All0.000009
ORF3a28F28del2TTt--t4345All0.000008
ORF3a28F28del2tTTt--145All0
ORF3a28F28del2TTT--N145All0
ORF3a28F28del1Ttt-tt3536All0.000007
ORF3a28F28del1TTt-Nt136All0
ORF3a28F28delTTT---3636B.1.1.70.000032
ORF3a28F28FttTttC3535AY.40.000054
ORF3a28F28LttTttA3535AY.4.40.014321
ORF3a28F28FttTttC3535B.1.1.70.000031
ORF3a28F28VTttGtt3133All0.000006
ORF3a28F28VTtTGtG233All0
ORF3a28F28delTTT---3030AY.250.00018
ORF3a28F28del2TTt--t2929B.1.214.20.017386
ORF3a28F28FttTttC2929B.1.617.20.000109
ORF3a28F28delTTT---2727AY.1190.000953
ORF3a28F28delTTT---2424B.1.10.000435
ORF3a28F28delTTT---2121AY.46.20.013342
ORF3a28F28delTTT---2020B.10.000183
ORF3a28F28LTttCtt1819AY.470.00056
ORF3a28F28LttTttA119AY.470.000031
ORF3a28F28StTttCt1818B.1.10.000327
ORF3a28F28LttTttA918B.1.617.20.000034
ORF3a28F28LTttCtt918B.1.617.20.000034
ORF3a28F28YtTttAt1517All0.000003
ORF3a28F28YtTTtAC217All0
ORF3a28F28delTTT---1515B.1.617.20.000056
ORF3a28F28delTTT---1414AY.290.000221
ORF3a28F28LttTttA1314AY.40.00002
ORF3a28F28LTttCtt114AY.40.000002
ORF3a28F28delTTT---1414AY.440.000085
ORF3a28F28delTTT---1313AY.1030.000081
ORF3a28F28delTTT---1313AY.1140.003004
ORF3a28F28delTTT---1313AY.30.000129
ORF3a28F28delTTT---1313AY.430.000058
ORF3a28F28delTTT---1313AY.450.001582
ORF3a28F28VTttGtt1313B.1.1.70.000012
ORF3a28F28delTTT---1313P.10.000205
ORF3a28F28ITttAtt1212B.1.1.70.000011
ORF3a28F28FttTttC1111AY.850.004699
ORF3a28F28ITttAtt1111B.1.1460.04661
ORF3a28F28del1Ttt-tt1111P.1.10.003494
ORF3a28F28CtTttGt1010All0.000002
ORF3a28F28delTTT---1010AY.3.10.000853
ORF3a28F28delTTT---99B.1.2100.01919
ORF3a28F28delTTT---99B.1.6390.195652
ORF3a28F28LTttCtt88AY.1030.00005
ORF3a28F28ITttAtt88AY.30.00008
ORF3a28F28delTTT---88AY.4.20.000174
ORF3a28F28FttTttC88AY.430.000035
ORF3a28F28LttTttA68AY.430.000027
ORF3a28F28LTttCtt28AY.430.000009
ORF3a28F28LttTttA88B.1.1.2240.114286
ORF3a28F28LttTttA88B.1.2580.000532
ORF3a28F28LTttCtt68P.10.000095
ORF3a28F28LttTttA28P.10.000032
ORF3a28F28GTTtGGt77All0.000001
ORF3a28F28delTTT---77AY.390.000173
ORF3a28F28YtTttAt77AY.430.000031
ORF3a28F28FttTttC77AY.630.002708
ORF3a28F28delTTT---77B.1.214.10.14
ORF3a28F28delTTT---66AY.230.000418
ORF3a28F28ITttAtt66B.10.000055
ORF3a28F28LTttCtt36B.10.000027
ORF3a28F28LttTttA26B.10.000018
ORF3a28F28LttTttG16B.10.000009
ORF3a28F28del1Ttt-tt66B.1.1.70.000005
ORF3a28F28delTTT---66B.1.1770.000079
ORF3a28F28GTTtGGt66B.1.214.20.003597
ORF3a28F28LttTttA66B.1.6370.000438
ORF3a28F28StTttCt55AY.40.000008
ORF3a28F28delTTT---55B.1.214.30.035714
ORF3a28F28LttTttA55B.1.4270.000252
ORF3a28F28YtTTtAC240.111111
ORF3a28F28HTTTCAC240.111111
ORF3a28F28HTTtCAt240.111111
ORF3a28F28LTttCtt240.111111
ORF3a28F28YtTttAt240.111111
ORF3a28F28LTtTCtC240.111111
ORF3a28F28HTTTCAC24All0
ORF3a28F28HTTtCAt24All0
ORF3a28F28LTttCtt44AY.1000.000184
ORF3a28F28FttTttC44AY.250.000024
ORF3a28F28delTTT---44AY.4.50.00043
ORF3a28F28LTttCtt44AY.46.40.000658
ORF3a28F28delTTT---44AY.50.000083
ORF3a28F28del2TTt--t44AY.50.000083
ORF3a28F28delTTT---44AY.5.30.00135
ORF3a28F28delTTT---44AY.99.20.000369
ORF3a28F28del1Ttt-tt44B.1.10.000073
ORF3a28F28LttTttA44B.1.1.2140.000222
ORF3a28F28LTttCtt24B.1.1600.000062
ORF3a28F28LttTttA24B.1.1600.000062
ORF3a28F28LTttCtt44B.1.160.100.032258
ORF3a28F28FttTttC44B.1.1770.000053
ORF3a28F28LTttCtt44B.1.1770.000053
ORF3a28F28LTttCtt44B.1.20.000035
ORF3a28F28delTTT---44B.1.2140.014652
ORF3a28F28FttTttC44B.1.2320.002149
ORF3a28F28delTTT---44B.1.617.10.000516
ORF3a28F28StTttCt44P.1.170.000647
ORF3a28F28ITttAtt330.166667
ORF3a28F28PTTtCCt23All0
ORF3a28F28PTTTCCC13All0
ORF3a28F28LttTttA23AY.250.000012
ORF3a28F28LTttCtt13AY.250.000006
ORF3a28F28VTttGtt33AY.260.000085
ORF3a28F28delTTT---33AY.330.0002
ORF3a28F28LTttCtt23AY.440.000012
ORF3a28F28LttTttG13AY.440.000006
ORF3a28F28delTTT---33AY.540.000286
ORF3a28F28LttTttA33AY.590.001589
ORF3a28F28LttTttA33AY.60.000123
ORF3a28F28LTttCtt33AY.750.000168
ORF3a28F28delTTT---33AY.880.002653
ORF3a28F28delTTT---33AY.9.20.00011
ORF3a28F28del1Ttt-tt33B.10.000027
ORF3a28F28LTttCtt33B.1.1.3110.001074
ORF3a28F28LTttCtt33B.1.1280.001906
ORF3a28F28FttTttC33B.1.20.000026
ORF3a28F28delTTT---33B.1.2180.015464
ORF3a28F28LTttCtt33B.1.4130.012766
ORF3a28F28LTttCtt33B.1.466.20.001174
ORF3a28F28StTttCt33B.1.4700.004213
ORF3a28F28delTTT---33B.1.6090.001438
ORF3a28F28StTttCt33B.1.617.20.000011
ORF3a28F28delTTT---33Q.10.000379
ORF3a28F28delTTT---33U.30.011583
ORF3a28F28FttTttC220.111111
ORF3a28F28delTTT---22AY.1020.000053
ORF3a28F28del2TTt--t22AY.1020.000053
ORF3a28F28ITttAtt22AY.1030.000012
ORF3a28F28LTttCtt22AY.1130.000285
ORF3a28F28delTTT---22AY.120.000632
ORF3a28F28delTTT---22AY.1200.000074
ORF3a28F28delTTT---22AY.130.000322
ORF3a28F28delTTT---22AY.220.004184
ORF3a28F28delTTT---22AY.260.000057
ORF3a28F28del2TTt--t22AY.30.00002
ORF3a28F28delTTT---22AY.39.10.000079
ORF3a28F28CtTttGt22AY.40.000003
ORF3a28F28FttTttC22AY.410.000588
ORF3a28F28delTTT---22AY.420.00008
ORF3a28F28LttTttA12AY.580.000907
ORF3a28F28LTttCtt12AY.580.000907
ORF3a28F28delTTT---22AY.70.000392
ORF3a28F28LTttCtt22AY.75.10.000361
ORF3a28F28VTttGtt22AY.790.002421
ORF3a28F28delTTT---22AY.810.003984
ORF3a28F28StTttCt22AY.830.003448
ORF3a28F28LttTttA22AY.930.000546
ORF3a28F28VTttGtt12B.10.000009
ORF3a28F28VTtTGtG12B.10.000009
ORF3a28F28FttTttC22B.1.10.000036
ORF3a28F28StTttCt22B.1.1.2770.001517
ORF3a28F28LttTttA22B.1.1.3060.000877
ORF3a28F28LTttCtt22B.1.1.3180.000604
ORF3a28F28LTttCtt22B.1.1.5190.000079
ORF3a28F28CtTttGt22B.1.1.70.000002
ORF3a28F28delTTT---22B.1.160.330.00885
ORF3a28F28delTTT---22B.1.177.830.002963
ORF3a28F28CtTttGt22B.1.214.20.001199
ORF3a28F28del1Ttt-tt12B.1.214.20.0006
ORF3a28F28del1TTt-Nt12B.1.214.20.0006
ORF3a28F28LTttCtt22B.1.2430.000139
ORF3a28F28LttTttA22B.1.4700.002809
ORF3a28F28LttTttA22B.1.5880.00182
ORF3a28F28YtTttAt22B.1.617.20.000008
ORF3a28F28VTttGtt22B.1.617.20.000008
ORF3a28F28StTttCt22B.1.6210.000177
ORF3a28F28FttTttC22D.20.00015
ORF3a28F28StTttCt22Q.80.00033
ORF3a28F28FttTttC11A.2.20.001689
ORF3a28F28LTttCtt11A.2.20.001689
ORF3a28F28delTTT---11A.23.10.000704
ORF3a28F28delTTT---11AY.1000.000046
ORF3a28F28YtTttAt11AY.1020.000027
ORF3a28F28FttTttC11AY.1030.000006
ORF3a28F28StTttCt11AY.1030.000006
ORF3a28F28CtTttGt11AY.1030.000006
ORF3a28F28FttTttC11AY.1100.000113
ORF3a28F28delTTT---11AY.1110.000183
ORF3a28F28VTttGtt11AY.1130.000142
ORF3a28F28ITttAtt11AY.1140.000231
ORF3a28F28LttTttG11AY.1170.000085
ORF3a28F28delTTT---11AY.1180.000063
ORF3a28F28del1Ttt-tt11AY.1200.000037
ORF3a28F28FttTttC11AY.1200.000037
ORF3a28F28delTTT---11AY.1210.000135
ORF3a28F28LttTttA11AY.1210.000135
ORF3a28F28FttTttC11AY.130.000161
ORF3a28F28delTTT---11AY.160.00038
ORF3a28F28LttTttA11AY.190.00114
ORF3a28F28delTTT---11AY.190.00114
ORF3a28F28delTTT---11AY.200.000039
ORF3a28F28LTttCtt11AY.200.000039
ORF3a28F28FttTttC11AY.230.00007
ORF3a28F28LttTttA11AY.230.00007
ORF3a28F28del1Ttt-tt11AY.250.000006
ORF3a28F28FttTttC11AY.260.000028
ORF3a28F28del1Ttt-tt11AY.30.00001
ORF3a28F28LTttCtt11AY.30.00001
ORF3a28F28FttTttC11AY.30.00001
ORF3a28F28LttTttA11AY.320.000532
ORF3a28F28delTTT---11AY.340.000097
ORF3a28F28del1Ttt-tt11AY.340.000097
ORF3a28F28FttTttC11AY.340.000097
ORF3a28F28FttTttC11AY.360.000148
ORF3a28F28delTTT---11AY.370.000316
ORF3a28F28StTttCt11AY.390.000025
ORF3a28F28FttTttC11AY.390.000025
ORF3a28F28del1Ttt-tt11AY.390.000025
ORF3a28F28del2TTt--t11AY.40.000002
ORF3a28F28del1Ttt-tt11AY.40.000002
ORF3a28F28delTTT---11AY.4.2.10.000149
ORF3a28F28FttTttC11AY.420.00004
ORF3a28F28LTttCtt11AY.420.00004
ORF3a28F28PTTtCCt11AY.430.000004
ORF3a28F28StTttCt11AY.430.000004
ORF3a28F28VTttGtt11AY.430.000004
ORF3a28F28YtTttAt11AY.440.000006
ORF3a28F28del2TTt--t11AY.440.000006
ORF3a28F28VTttGtt11AY.440.000006
ORF3a28F28FttTttC11AY.440.000006
ORF3a28F28StTttCt11AY.440.000006
ORF3a28F28YtTttAt11AY.460.000104
ORF3a28F28StTttCt11AY.460.000104
ORF3a28F28delTTT---11AY.460.000104
ORF3a28F28VTttGtt11AY.46.20.000635
ORF3a28F28LttTttG11AY.46.20.000635
ORF3a28F28delTTT---11AY.470.000031
ORF3a28F28ITttAtt11AY.470.000031
ORF3a28F28LttTttA11AY.5.30.000337
ORF3a28F28LTttCtt11AY.5.40.000277
ORF3a28F28del2TTt--t11AY.540.000095
ORF3a28F28delTTT---11AY.590.00053
ORF3a28F28StTttCt11AY.590.00053
ORF3a28F28del2TTt--t11AY.60.000041
ORF3a28F28delTTT---11AY.60.000041
ORF3a28F28delTTT---11AY.650.000533
ORF3a28F28FttTttC11AY.650.000533
ORF3a28F28delTTT---11AY.680.000274
ORF3a28F28FttTttC11AY.740.000116
ORF3a28F28VTttGtt11AY.750.000056
ORF3a28F28delTTT---11AY.750.000056
ORF3a28F28VTttGtt11AY.770.001127
ORF3a28F28LttTttA11AY.880.000884
ORF3a28F28LTttCtt11AY.9.20.000037
ORF3a28F28FttTttC11AY.920.000287
ORF3a28F28LTttCtt11AY.980.000079
ORF3a28F28delTTT---11AY.990.001049
ORF3a28F28LTtTCtA11AY.990.001049
ORF3a28F28delTTT---11B0.000128
ORF3a28F28StTttCt11B.10.000009
ORF3a28F28GTTtGGt11B.10.000009
ORF3a28F28CtTttGt11B.10.000009
ORF3a28F28CtTttGt11B.1.10.000018
ORF3a28F28VTttGtt11B.1.10.000018
ORF3a28F28delTTT---11B.1.1.1390.022727
ORF3a28F28FttTttC11B.1.1.1760.000439
ORF3a28F28delTTT---11B.1.1.1890.001513
ORF3a28F28delTTT---11B.1.1.2160.00089
ORF3a28F28LTttCtt11B.1.1.2160.00089
ORF3a28F28StTttCt11B.1.1.2220.000204
ORF3a28F28StTttCt11B.1.1.3110.000358
ORF3a28F28delTTT---11B.1.1.3110.000358
ORF3a28F28del1Ttt-tt11B.1.1.390.00051
ORF3a28F28delTTT---11B.1.1.4090.002833
ORF3a28F28LttTttA11B.1.1.4220.045455
ORF3a28F28delTTT---11B.1.1.4340.000349
ORF3a28F28del2TTt--t11B.1.1.5280.004808
ORF3a28F28LTttCtt11B.1.1.630.000386
ORF3a28F28del2tTTt--11B.1.1.70.000001
ORF3a28F28PTTTCCC11B.1.1.70.000001
ORF3a28F28StTttCt11B.1.1.890.006061
ORF3a28F28delTTT---11B.1.1530.018868
ORF3a28F28FttTttC11B.1.1600.000031
ORF3a28F28delTTT---11B.1.1600.000031
ORF3a28F28StTttCt11B.1.1770.000013
ORF3a28F28del1Ttt-tt11B.1.1770.000013
ORF3a28F28PTTtCCt11B.1.1770.000013
ORF3a28F28del2TTt--t11B.1.177.190.001431
ORF3a28F28delTTT---11B.1.177.210.000076
ORF3a28F28CtTttGt11B.1.177.210.000076
ORF3a28F28LTttCtt11B.1.177.440.000519
ORF3a28F28LTttCtt11B.1.177.580.001332
ORF3a28F28delTTT---11B.1.177.60.000977
ORF3a28F28del1Ttt-tt11B.1.177.80.000752
ORF3a28F28LttTttA11B.1.177.870.000728
ORF3a28F28StTttCt11B.1.177.870.000728
ORF3a28F28delTTT---11B.1.1790.003759
ORF3a28F28StTttCt11B.1.20.000009
ORF3a28F28VTttGtt11B.1.20.000009
ORF3a28F28StTttCt11B.1.2060.000816
ORF3a28F28VTttGtt11B.1.214.20.0006
ORF3a28F28del2TTT--N11B.1.2180.005155
ORF3a28F28LttTttA11B.1.2210.000071
ORF3a28F28del1Ttt-tt11B.1.2210.000071
ORF3a28F28StTttCt11B.1.2320.000537
ORF3a28F28StTttCt11B.1.2390.001221
ORF3a28F28delTTT---11B.1.2430.00007
ORF3a28F28delTTT---11B.1.2580.000067
ORF3a28F28YtTttAt11B.1.258.170.000104
ORF3a28F28LTttCtt11B.1.258.50.008772
ORF3a28F28LTttCtt11B.1.2980.002114
ORF3a28F28LttTttG11B.1.36.170.000494
ORF3a28F28FttTttC11B.1.36.180.00042
ORF3a28F28delTTT---11B.1.36.180.00042
ORF3a28F28LTttCtt11B.1.3610.001289
ORF3a28F28delTTT---11B.1.3890.001002
ORF3a28F28FttTttC11B.1.4130.004255
ORF3a28F28StTttCt11B.1.4270.00005
ORF3a28F28delTTT---11B.1.4270.00005
ORF3a28F28delTTT---11B.1.4590.004082
ORF3a28F28ITttAtt11B.1.5880.00091
ORF3a28F28ITttAtt11B.1.617.10.000129
ORF3a28F28LttTttA11B.1.617.10.000129
ORF3a28F28VTtTGtG11B.1.617.30.002985
ORF3a28F28delTTT---11B.1.6190.000871
ORF3a28F28LTttCtt11B.1.6210.000089
ORF3a28F28delTTT---11B.1.6380.052632
ORF3a28F28FttTttC11B.1.780.008547
ORF3a28F28delTTT---11B.550.00295
ORF3a28F28LTttCtt11B.60.00091
ORF3a28F28LttTttA11C.140.004329
ORF3a28F28delTTT---11C.160.00106
ORF3a28F28VTttGtt11C.370.000116
ORF3a28F28delTTT---11D.20.000075
ORF3a28F28ITttAtt11P.1.10.000318
ORF3a28F28delTTT---11P.1.150.000232
ORF3a28F28StTttCt11P.1.150.000232
ORF3a28F28LttTttG11Q.80.000165
ORF3a28F28StTttCt11R.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.