CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp4 : CodonNum = 354

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/nsp4354T354AT3117AnonsynActGct343234300.9994179614-9616
ORF1ab/nsp4354T354AT3117AnonsynAcTGcC343220.0005827519614-9616
ORF1ab/nsp4354T354IT3117InonsynaCtaTt8468450.9988189614-9616
ORF1ab/nsp4354T354IT3117InonsynaCTaTC84610.001182039614-9616
ORF1ab/nsp4354T354delT3117deldelACT---16916919614-9616
ORF1ab/nsp4354T354TT3117TsynacTacC104950.9134629614-9616
ORF1ab/nsp4354T354TT3117TsynacTacA10460.05769239614-9616
ORF1ab/nsp4354T354TT3117TsynacTacG10430.02884629614-9616
ORF1ab/nsp4354T354NT3117NnonsynaCtaAt878719614-9616
ORF1ab/nsp4354T354ST3117SnonsynaCtaGt1370.5384629614-9616
ORF1ab/nsp4354T354ST3117SnonsynaCTaGC1340.3076929614-9616
ORF1ab/nsp4354T354ST3117SnonsynActTct1320.1538469614-9616
ORF1ab/nsp4354T354del1T3117del1delacTac-730.4285719614-9616
ORF1ab/nsp4354T354del1T3117del1delAct-ct730.4285719614-9616
ORF1ab/nsp4354T354del1T3117del1delaCta-t710.1428579614-9616
ORF1ab/nsp4354T354FT3117FnonsynACtTTt320.6666679614-9616
ORF1ab/nsp4354T354FT3117FnonsynACTTTC310.3333339614-9616
ORF1ab/nsp4354T354PT3117PnonsynActCct2219614-9616
ORF1ab/nsp4354T354del2T3117del2delACT--G2219614-9616
ORF1ab/nsp4354T354VT3117VnonsynACtGTt1119614-9616
ORF1ab/nsp4354T354GT3117GnonsynACtGGt1119614-9616
ORF1ab/nsp4354T354RT3117RnonsynaCTaGG1119614-9616
ORF1ab/nsp4354T354LT3117LnonsynACtCTt1119614-9616

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/nsp4354T354AActGct34303432All0.000656
ORF1ab/nsp4354T354AAcTGcC23432All0
ORF1ab/nsp4354T354AActGct28062806B.1.6280.988724
ORF1ab/nsp4354T354IaCtaTt845846All0.000162
ORF1ab/nsp4354T354IaCTaTC1846All0
ORF1ab/nsp4354T354AActGct286286B.1.6340.979452
ORF1ab/nsp4354T354IaCtaTt229229AY.40.000356
ORF1ab/nsp4354T354delACT---169169All0.000032
ORF1ab/nsp4354T354TacTacC95104All0.000018
ORF1ab/nsp4354T354TacTacA6104All0.000001
ORF1ab/nsp4354T354TacTacG3104All0.000001
ORF1ab/nsp4354T354AActGct9898B.10.000898
ORF1ab/nsp4354T354delACT---8989B.1.1.70.00008
ORF1ab/nsp4354T354NaCtaAt8787All0.000017
ORF1ab/nsp4354T354AActGct8787B.1.1.70.000078
ORF1ab/nsp4354T354IaCtaTt5656AY.1200.002082
ORF1ab/nsp4354T354IaCtaTt5656B.1.1.70.00005
ORF1ab/nsp4354T354IaCtaTt4747AY.440.000286
ORF1ab/nsp4354T354AActGct3738AY.430.000164
ORF1ab/nsp4354T354AAcTGcC138AY.430.000004
ORF1ab/nsp4354T354TacTacC3737AY.340.003588
ORF1ab/nsp4354T354IaCtaTt3535AY.250.000211
ORF1ab/nsp4354T354IaCtaTt3535B.1.4270.001767
ORF1ab/nsp4354T354IaCtaTt2828B.1.617.20.000105
ORF1ab/nsp4354T354IaCtaTt2626AY.430.000115
ORF1ab/nsp4354T354IaCtaTt2020AY.1190.000706
ORF1ab/nsp4354T354IaCtaTt1919B.1.20.000167
ORF1ab/nsp4354T354IaCtaTt1818B.10.000165
ORF1ab/nsp4354T354IaCtaTt1818B.1.1.2220.003672
ORF1ab/nsp4354T354delACT---1818B.1.1770.000237
ORF1ab/nsp4354T354IaCtaTt1616B.1.2340.002111
ORF1ab/nsp4354T354IaCtaTt1515AY.1030.000093
ORF1ab/nsp4354T354AActGct1515AY.250.00009
ORF1ab/nsp4354T354NaCtaAt1515B.1.1.70.000013
ORF1ab/nsp4354T354NaCtaAt1515B.1.3510.000446
ORF1ab/nsp4354T354IaCtaTt1414AY.4.20.000304
ORF1ab/nsp4354T354SaCtaGt713All0.000001
ORF1ab/nsp4354T354SaCTaGC413All0.000001
ORF1ab/nsp4354T354SActTct213All0
ORF1ab/nsp4354T354TacTacC1313C.360.01184
ORF1ab/nsp4354T354TacTacC1212AY.440.000073
ORF1ab/nsp4354T354IaCtaTt1212B.1.10.000218
ORF1ab/nsp4354T354NaCtaAt1212B.1.20.000106
ORF1ab/nsp4354T354IaCtaTt1111AY.30.000109
ORF1ab/nsp4354T354IaCtaTt1111AY.39.10.000436
ORF1ab/nsp4354T354delACT---1111AY.40.000017
ORF1ab/nsp4354T354AActGct1010P.1.120.00484
ORF1ab/nsp4354T354IaCtaTt99B.1.4290.000212
ORF1ab/nsp4354T354NaCtaAt88AY.250.000048
ORF1ab/nsp4354T354IaCtaTt88AY.290.000126
ORF1ab/nsp4354T354delACT---88AY.4.50.00086
ORF1ab/nsp4354T354AActGct78AY.440.000043
ORF1ab/nsp4354T354AAcTGcC18AY.440.000006
ORF1ab/nsp4354T354IaCtaTt88B.1.1770.000105
ORF1ab/nsp4354T354AActGct88B.1.5580.03653
ORF1ab/nsp4354T354del1acTac-37All0.000001
ORF1ab/nsp4354T354del1Act-ct37All0.000001
ORF1ab/nsp4354T354del1aCta-t17All0
ORF1ab/nsp4354T354AActGct77AY.40.000011
ORF1ab/nsp4354T354AActGct77B.1.1.2040.021277
ORF1ab/nsp4354T354IaCtaTt77B.1.1600.000218
ORF1ab/nsp4354T354AActGct77B.1.617.20.000026
ORF1ab/nsp4354T354IaCtaTt66AY.200.000233
ORF1ab/nsp4354T354IaCtaTt66AY.4.50.000645
ORF1ab/nsp4354T354IaCtaTt66AY.50.000124
ORF1ab/nsp4354T354IaCtaTt66AY.98.10.000291
ORF1ab/nsp4354T354SaCTaGC450.222222
ORF1ab/nsp4354T354SActTct150.055556
ORF1ab/nsp4354T354IaCtaTt55AY.1020.000133
ORF1ab/nsp4354T354IaCtaTt55AY.1110.000916
ORF1ab/nsp4354T354IaCtaTt55AY.1180.000313
ORF1ab/nsp4354T354NaCtaAt55AY.260.000142
ORF1ab/nsp4354T354IaCtaTt55AY.390.000124
ORF1ab/nsp4354T354delACT---55AY.430.000022
ORF1ab/nsp4354T354IaCtaTt55AY.750.00028
ORF1ab/nsp4354T354del1Act-ct25B.1.1.70.000002
ORF1ab/nsp4354T354del1acTac-25B.1.1.70.000002
ORF1ab/nsp4354T354del1aCta-t15B.1.1.70.000001
ORF1ab/nsp4354T354AActGct55B.1.20.000044
ORF1ab/nsp4354T354TacTacC44AY.390.000099
ORF1ab/nsp4354T354NaCtaAt44AY.430.000018
ORF1ab/nsp4354T354AActGct44B.1.10.000073
ORF1ab/nsp4354T354TacTacC34B.1.1.70.000003
ORF1ab/nsp4354T354TacTacG14B.1.1.70.000001
ORF1ab/nsp4354T354delACT---44B.1.177.40.000844
ORF1ab/nsp4354T354TacTacC44B.1.20.000035
ORF1ab/nsp4354T354NaCtaAt44B.1.4290.000094
ORF1ab/nsp4354T354IaCtaTt44B.1.6210.000354
ORF1ab/nsp4354T354AActGct44B.1.6270.008081
ORF1ab/nsp4354T354FACtTTt23All0
ORF1ab/nsp4354T354FACTTTC13All0
ORF1ab/nsp4354T354IaCtaTt33AY.1060.001005
ORF1ab/nsp4354T354IaCtaTt33AY.1160.00086
ORF1ab/nsp4354T354TacTacC33AY.1170.000254
ORF1ab/nsp4354T354IaCtaTt33AY.240.001293
ORF1ab/nsp4354T354TacTacC33AY.250.000018
ORF1ab/nsp4354T354NaCtaAt33AY.330.0002
ORF1ab/nsp4354T354IaCtaTt33AY.420.000121
ORF1ab/nsp4354T354IaCtaTt33AY.46.60.000217
ORF1ab/nsp4354T354IaCtaTt33AY.640.001786
ORF1ab/nsp4354T354IaCtaTt33AY.950.002283
ORF1ab/nsp4354T354AActGct33B.1.1080.017442
ORF1ab/nsp4354T354AActGct33B.1.1770.00004
ORF1ab/nsp4354T354IaCtaTt33B.1.177.600.000655
ORF1ab/nsp4354T354IaCtaTt33B.1.177.810.000568
ORF1ab/nsp4354T354delACT---33B.1.177.870.002183
ORF1ab/nsp4354T354delACT---33B.1.20.000026
ORF1ab/nsp4354T354NaCtaAt33B.1.2580.0002
ORF1ab/nsp4354T354IaCtaTt33B.1.5170.001281
ORF1ab/nsp4354T354AActGct33B.1.5260.000071
ORF1ab/nsp4354T354delACT---33B.1.617.20.000011
ORF1ab/nsp4354T354TacTacC23B.1.617.20.000008
ORF1ab/nsp4354T354TacTacA13B.1.617.20.000004
ORF1ab/nsp4354T354IaCtaTt220.111111
ORF1ab/nsp4354T354del2ACT--G220.111111
ORF1ab/nsp4354T354FACtTTt220.111111
ORF1ab/nsp4354T354AActGct22A0.000774
ORF1ab/nsp4354T354del2ACT--G22All0
ORF1ab/nsp4354T354PActCct22All0
ORF1ab/nsp4354T354NaCtaAt22AY.1020.000053
ORF1ab/nsp4354T354AActGct22AY.1020.000053
ORF1ab/nsp4354T354NaCtaAt22AY.1030.000012
ORF1ab/nsp4354T354IaCtaTt22AY.230.000139
ORF1ab/nsp4354T354NaCtaAt22AY.40.000003
ORF1ab/nsp4354T354NaCtaAt22AY.610.00021
ORF1ab/nsp4354T354IaCtaTt22AY.70.000392
ORF1ab/nsp4354T354TacTacC22AY.9.20.000073
ORF1ab/nsp4354T354TacTacG12B.10.000009
ORF1ab/nsp4354T354TacTacC12B.10.000009
ORF1ab/nsp4354T354IaCtaTt22B.1.1.3170.000823
ORF1ab/nsp4354T354IaCtaTt22B.1.177.50.002484
ORF1ab/nsp4354T354AActGct22B.1.177.730.001133
ORF1ab/nsp4354T354IaCtaTt22B.1.177.860.000367
ORF1ab/nsp4354T354IaCtaTt22B.1.2580.000133
ORF1ab/nsp4354T354IaCtaTt22B.1.3510.000059
ORF1ab/nsp4354T354IaCtaTt22B.1.4780.023529
ORF1ab/nsp4354T354IaCtaTt22B.1.5250.000226
ORF1ab/nsp4354T354TacTacC22B.1.5950.000522
ORF1ab/nsp4354T354AActGct22B.1.5960.000174
ORF1ab/nsp4354T354IaCtaTt22B.1.6180.008065
ORF1ab/nsp4354T354TacTacA22D.20.00015
ORF1ab/nsp4354T354IaCtaTt22P.10.000032
ORF1ab/nsp4354T354AActGct22P.10.000032
ORF1ab/nsp4354T354IaCtaTt22P.20.000373
ORF1ab/nsp4354T354IaCtaTt11A.10.000282
ORF1ab/nsp4354T354AActGct11A.270.001656
ORF1ab/nsp4354T354IaCtaTt11A.270.001656
ORF1ab/nsp4354T354delACT---11AD.20.000219
ORF1ab/nsp4354T354LACtCTt11All0
ORF1ab/nsp4354T354GACtGGt11All0
ORF1ab/nsp4354T354RaCTaGG11All0
ORF1ab/nsp4354T354VACtGTt11All0
ORF1ab/nsp4354T354NaCtaAt11AY.10.000396
ORF1ab/nsp4354T354NaCtaAt11AY.1000.000046
ORF1ab/nsp4354T354AActGct11AY.1030.000006
ORF1ab/nsp4354T354delACT---11AY.1110.000183
ORF1ab/nsp4354T354IaCtaTt11AY.1170.000085
ORF1ab/nsp4354T354IaCtaTt11AY.1210.000135
ORF1ab/nsp4354T354delACT---11AY.190.00114
ORF1ab/nsp4354T354TacTacC11AY.200.000039
ORF1ab/nsp4354T354TacTacC11AY.230.00007
ORF1ab/nsp4354T354NaCtaAt11AY.270.000065
ORF1ab/nsp4354T354TacTacC11AY.290.000016
ORF1ab/nsp4354T354AActGct11AY.290.000016
ORF1ab/nsp4354T354IaCtaTt11AY.3.10.000085
ORF1ab/nsp4354T354IaCtaTt11AY.330.000067
ORF1ab/nsp4354T354AActGct11AY.390.000025
ORF1ab/nsp4354T354AActGct11AY.39.20.001541
ORF1ab/nsp4354T354del1acTac-11AY.40.000002
ORF1ab/nsp4354T354TacTacG11AY.40.000002
ORF1ab/nsp4354T354VACtGTt11AY.4.20.000022
ORF1ab/nsp4354T354AActGct11AY.420.00004
ORF1ab/nsp4354T354IaCtaTt11AY.460.000104
ORF1ab/nsp4354T354delACT---11AY.46.20.000635
ORF1ab/nsp4354T354IaCtaTt11AY.470.000031
ORF1ab/nsp4354T354AActGct11AY.50.000021
ORF1ab/nsp4354T354NaCtaAt11AY.540.000095
ORF1ab/nsp4354T354delACT---11AY.60.000041
ORF1ab/nsp4354T354delACT---11AY.600.000938
ORF1ab/nsp4354T354IaCTaTC11AY.670.000464
ORF1ab/nsp4354T354IaCtaTt11AY.680.000274
ORF1ab/nsp4354T354delACT---11AY.680.000274
ORF1ab/nsp4354T354IaCtaTt11AY.80.000606
ORF1ab/nsp4354T354delACT---11AY.90.000068
ORF1ab/nsp4354T354TacTacC11AY.990.001049
ORF1ab/nsp4354T354IaCtaTt11AY.990.001049
ORF1ab/nsp4354T354delACT---11AY.99.10.001553
ORF1ab/nsp4354T354IaCtaTt11AY.99.20.000092
ORF1ab/nsp4354T354IaCtaTt11B0.000128
ORF1ab/nsp4354T354NaCtaAt11B.10.000009
ORF1ab/nsp4354T354SaCtaGt11B.10.000009
ORF1ab/nsp4354T354GACtGGt11B.10.000009
ORF1ab/nsp4354T354FACTTTC11B.1.10.000018
ORF1ab/nsp4354T354NaCtaAt11B.1.10.000018
ORF1ab/nsp4354T354delACT---11B.1.10.000018
ORF1ab/nsp4354T354AActGct11B.1.1.1170.009709
ORF1ab/nsp4354T354delACT---11B.1.1.1390.022727
ORF1ab/nsp4354T354AActGct11B.1.1.2200.001859
ORF1ab/nsp4354T354IaCtaTt11B.1.1.250.000569
ORF1ab/nsp4354T354PActCct11B.1.1.250.000569
ORF1ab/nsp4354T354LACtCTt11B.1.1.250.000569
ORF1ab/nsp4354T354SActTct11B.1.1.2540.011236
ORF1ab/nsp4354T354IaCtaTt11B.1.1.2620.015152
ORF1ab/nsp4354T354NaCtaAt11B.1.1.2840.000107
ORF1ab/nsp4354T354IaCtaTt11B.1.1.3110.000358
ORF1ab/nsp4354T354delACT---11B.1.1.3120.001912
ORF1ab/nsp4354T354AActGct11B.1.1.330.000421
ORF1ab/nsp4354T354IaCtaTt11B.1.1.390.00051
ORF1ab/nsp4354T354AActGct11B.1.1.4130.006897
ORF1ab/nsp4354T354AActGct11B.1.1.4290.004608
ORF1ab/nsp4354T354IaCtaTt11B.1.1.4590.015385
ORF1ab/nsp4354T354delACT---11B.1.1.510.001718
ORF1ab/nsp4354T354SaCtaGt11B.1.1.5190.00004
ORF1ab/nsp4354T354PActCct11B.1.1.70.000001
ORF1ab/nsp4354T354SaCtaGt11B.1.1.70.000001
ORF1ab/nsp4354T354delACT---11B.1.1.700.000341
ORF1ab/nsp4354T354AActGct11B.1.1280.000635
ORF1ab/nsp4354T354IaCtaTt11B.1.1280.000635
ORF1ab/nsp4354T354TacTacA11B.1.1600.000031
ORF1ab/nsp4354T354del1Act-ct11B.1.1770.000013
ORF1ab/nsp4354T354TacTacC11B.1.1770.000013
ORF1ab/nsp4354T354delACT---11B.1.177.160.000664
ORF1ab/nsp4354T354delACT---11B.1.177.170.000821
ORF1ab/nsp4354T354delACT---11B.1.177.180.00116
ORF1ab/nsp4354T354IaCtaTt11B.1.177.440.000519
ORF1ab/nsp4354T354TacTacA11B.1.177.570.000281
ORF1ab/nsp4354T354delACT---11B.1.177.690.001484
ORF1ab/nsp4354T354IaCtaTt11B.1.177.750.001041
ORF1ab/nsp4354T354delACT---11B.1.177.760.002494
ORF1ab/nsp4354T354delACT---11B.1.177.860.000183
ORF1ab/nsp4354T354IaCtaTt11B.1.177.870.000728
ORF1ab/nsp4354T354IaCtaTt11B.1.214.20.0006
ORF1ab/nsp4354T354IaCtaTt11B.1.2180.005155
ORF1ab/nsp4354T354TacTacC11B.1.2210.000071
ORF1ab/nsp4354T354AActGct11B.1.2210.000071
ORF1ab/nsp4354T354SaCtaGt11B.1.221.30.000833
ORF1ab/nsp4354T354AActGct11B.1.2320.000537
ORF1ab/nsp4354T354NaCtaAt11B.1.2340.000132
ORF1ab/nsp4354T354AActGct11B.1.2430.00007
ORF1ab/nsp4354T354AActGct11B.1.2470.014925
ORF1ab/nsp4354T354delACT---11B.1.2580.000067
ORF1ab/nsp4354T354SaCtaGt11B.1.258.50.008772
ORF1ab/nsp4354T354IaCtaTt11B.1.3110.000275
ORF1ab/nsp4354T354IaCtaTt11B.1.3490.000715
ORF1ab/nsp4354T354IaCtaTt11B.1.351.30.000876
ORF1ab/nsp4354T354TacTacC11B.1.351.50.0006
ORF1ab/nsp4354T354IaCtaTt11B.1.360.000146
ORF1ab/nsp4354T354TacTacA11B.1.36.160.001425
ORF1ab/nsp4354T354AActGct11B.1.3750.00082
ORF1ab/nsp4354T354IaCtaTt11B.1.3890.001002
ORF1ab/nsp4354T354IaCtaTt11B.1.4130.004255
ORF1ab/nsp4354T354SaCtaGt11B.1.4290.000024
ORF1ab/nsp4354T354IaCtaTt11B.1.4670.04
ORF1ab/nsp4354T354NaCtaAt11B.1.5260.000024
ORF1ab/nsp4354T354IaCtaTt11B.1.5820.000491
ORF1ab/nsp4354T354TacTacC11B.1.6090.000479
ORF1ab/nsp4354T354RaCTaGG11B.1.617.20.000004
ORF1ab/nsp4354T354AActGct11B.1.6190.000871
ORF1ab/nsp4354T354AActGct11B.1.6210.000089
ORF1ab/nsp4354T354NaCtaAt11B.1.6370.000073
ORF1ab/nsp4354T354delACT---11B.150.017544
ORF1ab/nsp4354T354IaCtaTt11B.4.50.011905
ORF1ab/nsp4354T354IaCtaTt11B.400.000364
ORF1ab/nsp4354T354delACT---11C.170.055556
ORF1ab/nsp4354T354delACT---11C.350.000774
ORF1ab/nsp4354T354AActGct11C.370.000116
ORF1ab/nsp4354T354IaCtaTt11D.20.000075
ORF1ab/nsp4354T354SaCtaGt11P.10.000016
ORF1ab/nsp4354T354IaCtaTt11P.1.10.000318
ORF1ab/nsp4354T354AActGct11P.20.000187
ORF1ab/nsp4354T354IaCtaTt11Q.10.000126
ORF1ab/nsp4354T354delACT---11Q.10.000126
ORF1ab/nsp4354T354AActGct11Q.30.000145
ORF1ab/nsp4354T354IaCtaTt11Q.80.000165
ORF1ab/nsp4354T354TacTacC11R.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.