CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 543

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/nsp3543S543PS1361PnonsynTctCct100161001614346-4348
ORF1ab/nsp3543S543FS1361FnonsyntCttTt93493414346-4348
ORF1ab/nsp3543S543SS1361SsyntcTtcC1751250.7142864346-4348
ORF1ab/nsp3543S543SS1361SsyntcTtcG175380.2171434346-4348
ORF1ab/nsp3543S543SS1361SsyntcTtcA175120.06857144346-4348
ORF1ab/nsp3543S543AS1361AnonsynTctGct636314346-4348
ORF1ab/nsp3543S543YS1361YnonsyntCttAt383814346-4348
ORF1ab/nsp3543S543delS1361deldelTCT---333314346-4348
ORF1ab/nsp3543S543TS1361TnonsynTctAct212114346-4348
ORF1ab/nsp3543S543CS1361CnonsyntCttGt121214346-4348
ORF1ab/nsp3543S543del1S1361del1delTct-ct210.54346-4348
ORF1ab/nsp3543S543del1S1361del1delTCTCT-210.54346-4348
ORF1ab/nsp3543S543LS1361LnonsynTCtCTt1114346-4348
ORF1ab/nsp3543S543del2S1361del2deltCTt--1114346-4348
ORF1ab/nsp3543S543DS1361DnonsynTCtGAt1114346-4348

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/nsp3543S543PTctCct1001610016All0.001916
ORF1ab/nsp3543S543PTctCct93109310B.1.1.2840.999893
ORF1ab/nsp3543S543FtCttTt934934All0.000179
ORF1ab/nsp3543S543FtCttTt315315B.1.1.70.000282
ORF1ab/nsp3543S543PTctCct203203AY.470.006314
ORF1ab/nsp3543S543StcTtcC125175All0.000024
ORF1ab/nsp3543S543StcTtcG38175All0.000007
ORF1ab/nsp3543S543StcTtcA12175All0.000002
ORF1ab/nsp3543S543PTctCct126126B.1.10.002286
ORF1ab/nsp3543S543ATctGct6363All0.000012
ORF1ab/nsp3543S543FtCttTt6161AY.1030.000379
ORF1ab/nsp3543S543PTctCct6060B.1.5260.00141
ORF1ab/nsp3543S543PTctCct4949B.1.2430.00341
ORF1ab/nsp3543S543FtCttTt4949B.1.617.20.000185
ORF1ab/nsp3543S543FtCttTt4444AY.1200.001636
ORF1ab/nsp3543S543StcTtcC3743B.1.1.70.000033
ORF1ab/nsp3543S543StcTtcG443B.1.1.70.000004
ORF1ab/nsp3543S543StcTtcA243B.1.1.70.000002
ORF1ab/nsp3543S543FtCttTt4141AY.40.000064
ORF1ab/nsp3543S543YtCttAt3838All0.000007
ORF1ab/nsp3543S543delTCT---3333All0.000006
ORF1ab/nsp3543S543StcTtcG3133B.1.4270.001565
ORF1ab/nsp3543S543StcTtcC233B.1.4270.000101
ORF1ab/nsp3543S543FtCttTt3232P.10.000504
ORF1ab/nsp3543S543PTctCct3131B.1.617.20.000117
ORF1ab/nsp3543S543PTctCct3030B.1.1.1600.714286
ORF1ab/nsp3543S543PTctCct2626B.1.1.70.000023
ORF1ab/nsp3543S543FtCttTt2424B.1.20.000211
ORF1ab/nsp3543S543PTctCct2323B.10.000211
ORF1ab/nsp3543S543FtCttTt2323P.1.70.007344
ORF1ab/nsp3543S543TTctAct2121All0.000004
ORF1ab/nsp3543S543PTctCct2121B.1.360.003064
ORF1ab/nsp3543S543FtCttTt2020AY.430.000089
ORF1ab/nsp3543S543YtCttAt1919B.1.1.70.000017
ORF1ab/nsp3543S543FtCttTt1818AY.80.010909
ORF1ab/nsp3543S543ATctGct1818B.1.1.70.000016
ORF1ab/nsp3543S543FtCttTt1818B.1.4290.000424
ORF1ab/nsp3543S543PTctCct1818B.1.6370.001315
ORF1ab/nsp3543S543FtCttTt1717AY.1020.000451
ORF1ab/nsp3543S543PTctCct1717AY.40.000026
ORF1ab/nsp3543S543StcTtcC1416AY.40.000022
ORF1ab/nsp3543S543StcTtcA216AY.40.000003
ORF1ab/nsp3543S543delTCT---1616B.1.1.70.000014
ORF1ab/nsp3543S543FtCttTt1515AY.250.00009
ORF1ab/nsp3543S543FtCttTt1515B.1.177.620.017878
ORF1ab/nsp3543S543FtCttTt1515B.1.36.290.00776
ORF1ab/nsp3543S543ATctGct1414AD.20.003065
ORF1ab/nsp3543S543FtCttTt1313B.1.2210.000923
ORF1ab/nsp3543S543FtCttTt1313B.1.5250.001471
ORF1ab/nsp3543S543CtCttGt1212All0.000002
ORF1ab/nsp3543S543FtCttTt1212AY.4.20.00026
ORF1ab/nsp3543S543FtCttTt1212B.1.1770.000158
ORF1ab/nsp3543S543StcTtcC1111B.1.5260.000259
ORF1ab/nsp3543S543FtCttTt1111P.1.140.000526
ORF1ab/nsp3543S543FtCttTt99AY.1000.000414
ORF1ab/nsp3543S543FtCttTt99B.10.000082
ORF1ab/nsp3543S543CtCttGt88B.10.000073
ORF1ab/nsp3543S543PTctCct88B.1.1.1350.037559
ORF1ab/nsp3543S543FtCttTt88B.1.2580.000532
ORF1ab/nsp3543S543FtCttTt77AY.10.00277
ORF1ab/nsp3543S543FtCttTt77AY.30.00007
ORF1ab/nsp3543S543FtCttTt77AY.520.0057
ORF1ab/nsp3543S543FtCttTt77B.1.5260.000165
ORF1ab/nsp3543S543StcTtcC77P.1.140.000335
ORF1ab/nsp3543S543PTctCct66AY.1030.000037
ORF1ab/nsp3543S543PTctCct66AY.1130.000854
ORF1ab/nsp3543S543FtCttTt66AY.440.000037
ORF1ab/nsp3543S543FtCttTt66B.1.1.3690.002677
ORF1ab/nsp3543S543FtCttTt66B.1.258.170.000624
ORF1ab/nsp3543S543StcTtcC46B.1.4290.000094
ORF1ab/nsp3543S543StcTtcG26B.1.4290.000047
ORF1ab/nsp3543S543StcTtcC66B.1.617.20.000023
ORF1ab/nsp3543S543PTctCct66B.1.6210.000531
ORF1ab/nsp3543S543FtCttTt55AY.1190.000177
ORF1ab/nsp3543S543FtCttTt55AY.260.000142
ORF1ab/nsp3543S543PTctCct55AY.46.60.000361
ORF1ab/nsp3543S543FtCttTt55AY.50.000103
ORF1ab/nsp3543S543TTctAct55B.1.2580.000333
ORF1ab/nsp3543S543PTctCct44AY.290.000063
ORF1ab/nsp3543S543delTCT---44AY.40.000006
ORF1ab/nsp3543S543StcTtcC34AY.440.000018
ORF1ab/nsp3543S543StcTtcG14AY.440.000006
ORF1ab/nsp3543S543FtCttTt44AY.470.000124
ORF1ab/nsp3543S543StcTtcA34B.10.000027
ORF1ab/nsp3543S543StcTtcC14B.10.000009
ORF1ab/nsp3543S543TTctAct44B.1.1.1700.004988
ORF1ab/nsp3543S543StcTtcC44B.1.1.5190.000159
ORF1ab/nsp3543S543StcTtcC44B.1.20.000035
ORF1ab/nsp3543S543FtCttTt44B.1.3510.000119
ORF1ab/nsp3543S543ATctGct44B.1.617.20.000015
ORF1ab/nsp3543S543FtCttTt33AD.20.000657
ORF1ab/nsp3543S543PTctCct33AD.20.000657
ORF1ab/nsp3543S543StcTtcC33AY.240.001293
ORF1ab/nsp3543S543StcTtcC33AY.250.000018
ORF1ab/nsp3543S543TTctAct33AY.370.000948
ORF1ab/nsp3543S543StcTtcA23AY.390.000049
ORF1ab/nsp3543S543StcTtcC13AY.390.000025
ORF1ab/nsp3543S543FtCttTt33AY.4.40.001227
ORF1ab/nsp3543S543delTCT---33AY.4.50.000322
ORF1ab/nsp3543S543PTctCct33AY.420.000121
ORF1ab/nsp3543S543ATctGct33AY.440.000018
ORF1ab/nsp3543S543PTctCct33AY.440.000018
ORF1ab/nsp3543S543PTctCct33AY.750.000168
ORF1ab/nsp3543S543PTctCct33AY.960.006224
ORF1ab/nsp3543S543FtCttTt33B.1.10.000054
ORF1ab/nsp3543S543PTctCct33B.1.1.2070.003546
ORF1ab/nsp3543S543PTctCct33B.1.1.2530.007519
ORF1ab/nsp3543S543TTctAct33B.1.1.70.000003
ORF1ab/nsp3543S543delTCT---33B.1.1770.00004
ORF1ab/nsp3543S543PTctCct33B.1.1770.00004
ORF1ab/nsp3543S543PTctCct33B.1.20.000026
ORF1ab/nsp3543S543FtCttTt33B.1.3110.000824
ORF1ab/nsp3543S543FtCttTt33B.1.360.000438
ORF1ab/nsp3543S543ATctGct33B.1.5260.000071
ORF1ab/nsp3543S543YtCttAt33B.1.617.20.000011
ORF1ab/nsp3543S543ATctGct33B.1.6210.000266
ORF1ab/nsp3543S543PTctCct33C.370.000348
ORF1ab/nsp3543S543del1TCTCT-12All0
ORF1ab/nsp3543S543del1Tct-ct12All0
ORF1ab/nsp3543S543FtCttTt22AY.100.00106
ORF1ab/nsp3543S543PTctCct22AY.1000.000092
ORF1ab/nsp3543S543FtCttTt22AY.1180.000125
ORF1ab/nsp3543S543StcTtcC22AY.230.000139
ORF1ab/nsp3543S543PTctCct22AY.250.000012
ORF1ab/nsp3543S543FtCttTt22AY.330.000134
ORF1ab/nsp3543S543FtCttTt22AY.390.000049
ORF1ab/nsp3543S543PTctCct22AY.390.000049
ORF1ab/nsp3543S543FtCttTt22AY.39.10.000079
ORF1ab/nsp3543S543FtCttTt22AY.410.000588
ORF1ab/nsp3543S543FtCttTt22AY.450.000243
ORF1ab/nsp3543S543FtCttTt22AY.490.00639
ORF1ab/nsp3543S543FtCttTt22AY.7.20.001119
ORF1ab/nsp3543S543PTctCct22AY.98.10.000097
ORF1ab/nsp3543S543ATctGct22B.10.000018
ORF1ab/nsp3543S543YtCttAt22B.10.000018
ORF1ab/nsp3543S543TTctAct22B.10.000018
ORF1ab/nsp3543S543YtCttAt22B.1.10.000036
ORF1ab/nsp3543S543PTctCct22B.1.1.560.035714
ORF1ab/nsp3543S543ATctGct22B.1.1600.000062
ORF1ab/nsp3543S543StcTtcC22B.1.1770.000026
ORF1ab/nsp3543S543YtCttAt22B.1.2340.000264
ORF1ab/nsp3543S543CtCttGt22B.1.3670.001585
ORF1ab/nsp3543S543FtCttTt22B.1.5640.000852
ORF1ab/nsp3543S543ATctGct22B.1.5680.002222
ORF1ab/nsp3543S543StcTtcC22P.10.000032
ORF1ab/nsp3543S543FtCttTt22W.10.017391
ORF1ab/nsp3543S543FtCttTt11A0.000387
ORF1ab/nsp3543S543FtCttTt11A.10.000282
ORF1ab/nsp3543S543StcTtcC11A.20.000662
ORF1ab/nsp3543S543del2tCTt--11All0
ORF1ab/nsp3543S543LTCtCTt11All0
ORF1ab/nsp3543S543DTCtGAt11All0
ORF1ab/nsp3543S543StcTtcC11AY.1000.000046
ORF1ab/nsp3543S543ATctGct11AY.1030.000006
ORF1ab/nsp3543S543delTCT---11AY.1030.000006
ORF1ab/nsp3543S543FtCttTt11AY.1110.000183
ORF1ab/nsp3543S543delTCT---11AY.1110.000183
ORF1ab/nsp3543S543FtCttTt11AY.1170.000085
ORF1ab/nsp3543S543PTctCct11AY.1190.000035
ORF1ab/nsp3543S543del1TCTCT-11AY.1200.000037
ORF1ab/nsp3543S543FtCttTt11AY.1210.000135
ORF1ab/nsp3543S543FtCttTt11AY.130.000161
ORF1ab/nsp3543S543PTctCct11AY.140.000088
ORF1ab/nsp3543S543FtCttTt11AY.16.10.00047
ORF1ab/nsp3543S543FtCttTt11AY.20.000356
ORF1ab/nsp3543S543FtCttTt11AY.200.000039
ORF1ab/nsp3543S543PTctCct11AY.200.000039
ORF1ab/nsp3543S543FtCttTt11AY.230.00007
ORF1ab/nsp3543S543CtCttGt11AY.250.000006
ORF1ab/nsp3543S543ATctGct11AY.250.000006
ORF1ab/nsp3543S543YtCttAt11AY.260.000028
ORF1ab/nsp3543S543StcTtcC11AY.290.000016
ORF1ab/nsp3543S543StcTtcC11AY.30.00001
ORF1ab/nsp3543S543PTctCct11AY.320.000532
ORF1ab/nsp3543S543PTctCct11AY.34.10.00051
ORF1ab/nsp3543S543ATctGct11AY.40.000002
ORF1ab/nsp3543S543StcTtcC11AY.4.20.000022
ORF1ab/nsp3543S543PTctCct11AY.4.2.10.000149
ORF1ab/nsp3543S543PTctCct11AY.4.30.000842
ORF1ab/nsp3543S543FtCttTt11AY.420.00004
ORF1ab/nsp3543S543ATctGct11AY.430.000004
ORF1ab/nsp3543S543PTctCct11AY.430.000004
ORF1ab/nsp3543S543LTCtCTt11AY.440.000006
ORF1ab/nsp3543S543TTctAct11AY.440.000006
ORF1ab/nsp3543S543PTctCct11AY.450.000122
ORF1ab/nsp3543S543ATctGct11AY.470.000031
ORF1ab/nsp3543S543YtCttAt11AY.50.000021
ORF1ab/nsp3543S543StcTtcC11AY.50.000021
ORF1ab/nsp3543S543FtCttTt11AY.580.000907
ORF1ab/nsp3543S543YtCttAt11AY.610.000105
ORF1ab/nsp3543S543FtCttTt11AY.650.000533
ORF1ab/nsp3543S543PTctCct11AY.650.000533
ORF1ab/nsp3543S543FtCttTt11AY.670.000464
ORF1ab/nsp3543S543PTctCct11AY.910.00073
ORF1ab/nsp3543S543FtCttTt11AY.99.20.000092
ORF1ab/nsp3543S543YtCttAt11AY.99.20.000092
ORF1ab/nsp3543S543StcTtcC11B0.000128
ORF1ab/nsp3543S543del1Tct-ct11B.10.000009
ORF1ab/nsp3543S543StcTtcC11B.1.10.000018
ORF1ab/nsp3543S543FtCttTt11B.1.1.2140.000055
ORF1ab/nsp3543S543PTctCct11B.1.1.2360.006897
ORF1ab/nsp3543S543StcTtcC11B.1.1.250.000569
ORF1ab/nsp3543S543PTctCct11B.1.1.2770.000759
ORF1ab/nsp3543S543PTctCct11B.1.1.2910.000742
ORF1ab/nsp3543S543ATctGct11B.1.1.2940.001266
ORF1ab/nsp3543S543StcTtcC11B.1.1.2940.001266
ORF1ab/nsp3543S543PTctCct11B.1.1.3660.015873
ORF1ab/nsp3543S543PTctCct11B.1.1.370.000193
ORF1ab/nsp3543S543FtCttTt11B.1.1.4290.004608
ORF1ab/nsp3543S543StcTtcC11B.1.1.4340.000349
ORF1ab/nsp3543S543PTctCct11B.1.1.4480.002033
ORF1ab/nsp3543S543FtCttTt11B.1.1.500.000679
ORF1ab/nsp3543S543StcTtcC11B.1.1.500.000679
ORF1ab/nsp3543S543YtCttAt11B.1.1.500.000679
ORF1ab/nsp3543S543delTCT---11B.1.1.5190.00004
ORF1ab/nsp3543S543ATctGct11B.1.1.5190.00004
ORF1ab/nsp3543S543StcTtcC11B.1.1.630.000386
ORF1ab/nsp3543S543del2tCTt--11B.1.1.70.000001
ORF1ab/nsp3543S543YtCttAt11B.1.1180.006711
ORF1ab/nsp3543S543FtCttTt11B.1.1260.001276
ORF1ab/nsp3543S543delTCT---11B.1.1600.000031
ORF1ab/nsp3543S543YtCttAt11B.1.1770.000013
ORF1ab/nsp3543S543FtCttTt11B.1.177.210.000076
ORF1ab/nsp3543S543StcTtcC11B.1.177.600.000218
ORF1ab/nsp3543S543FtCttTt11B.1.177.600.000218
ORF1ab/nsp3543S543ATctGct11B.1.20.000009
ORF1ab/nsp3543S543FtCttTt11B.1.214.20.0006
ORF1ab/nsp3543S543ATctGct11B.1.2220.001692
ORF1ab/nsp3543S543PTctCct11B.1.2400.000216
ORF1ab/nsp3543S543StcTtcA11B.1.2580.000067
ORF1ab/nsp3543S543PTctCct11B.1.258.170.000104
ORF1ab/nsp3543S543ATctGct11B.1.2600.003344
ORF1ab/nsp3543S543PTctCct11B.1.2940.032258
ORF1ab/nsp3543S543StcTtcC11B.1.3010.005917
ORF1ab/nsp3543S543StcTtcA11B.1.3320.003497
ORF1ab/nsp3543S543YtCttAt11B.1.3510.00003
ORF1ab/nsp3543S543FtCttTt11B.1.351.20.000303
ORF1ab/nsp3543S543YtCttAt11B.1.351.20.000303
ORF1ab/nsp3543S543FtCttTt11B.1.351.50.0006
ORF1ab/nsp3543S543delTCT---11B.1.360.000146
ORF1ab/nsp3543S543StcTtcC11B.1.360.000146
ORF1ab/nsp3543S543PTctCct11B.1.36.220.001208
ORF1ab/nsp3543S543FtCttTt11B.1.3610.001289
ORF1ab/nsp3543S543FtCttTt11B.1.4090.000781
ORF1ab/nsp3543S543delTCT---11B.1.4150.014286
ORF1ab/nsp3543S543TTctAct11B.1.4290.000024
ORF1ab/nsp3543S543DTCtGAt11B.1.4620.007246
ORF1ab/nsp3543S543FtCttTt11B.1.466.10.007194
ORF1ab/nsp3543S543YtCttAt11B.1.4730.019231
ORF1ab/nsp3543S543FtCttTt11B.1.4740.001901
ORF1ab/nsp3543S543PTctCct11B.1.5030.002488
ORF1ab/nsp3543S543ATctGct11B.1.5250.000113
ORF1ab/nsp3543S543StcTtcC11B.1.5250.000113
ORF1ab/nsp3543S543PTctCct11B.1.5810.009434
ORF1ab/nsp3543S543FtCttTt11B.1.5850.027778
ORF1ab/nsp3543S543PTctCct11B.1.5870.001898
ORF1ab/nsp3543S543StcTtcC11B.1.5950.000261
ORF1ab/nsp3543S543StcTtcA11B.1.5960.000087
ORF1ab/nsp3543S543FtCttTt11B.1.5960.000087
ORF1ab/nsp3543S543FtCttTt11B.1.6090.000479
ORF1ab/nsp3543S543delTCT---11B.1.617.20.000004
ORF1ab/nsp3543S543StcTtcC11B.1.6210.000089
ORF1ab/nsp3543S543PTctCct11B.1.6280.000352
ORF1ab/nsp3543S543PTctCct11B.1.80.001972
ORF1ab/nsp3543S543CtCttGt11B.30.000831
ORF1ab/nsp3543S543FtCttTt11B.400.000364
ORF1ab/nsp3543S543FtCttTt11D.20.000075
ORF1ab/nsp3543S543TTctAct11P.10.000016
ORF1ab/nsp3543S543ATctGct11P.10.000016
ORF1ab/nsp3543S543FtCttTt11P.1.100.000269
ORF1ab/nsp3543S543TTctAct11P.1.140.000048
ORF1ab/nsp3543S543PTctCct11P.1.140.000048

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.