CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 200 & Codon = cTt

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/nsp2200P200LP380LnonsyncCtcTt17000169780.9987061403-1405

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/nsp2200P200LcCtcTt1697817000All0.003247
ORF1ab/nsp2200P200LcCtcTt1194011961AY.230.83281
ORF1ab/nsp2200P200LcCtcTt23912391AY.23.10.997913
ORF1ab/nsp2200P200LcCtcTt722722B.1.3510.021463
ORF1ab/nsp2200P200LcCtcTt578578AY.40.0009
ORF1ab/nsp2200P200LcCtcTt273273AY.1160.078291
ORF1ab/nsp2200P200LcCtcTt201201B.1.1.70.00018
ORF1ab/nsp2200P200LcCtcTt8484AY.440.000511
ORF1ab/nsp2200P200LcCtcTt8181AY.1200.003011
ORF1ab/nsp2200P200LcCtcTt6161P.10.000961
ORF1ab/nsp2200P200LcCtcTt4849B.1.20.000423
ORF1ab/nsp2200P200LcCtcTt4343B.1.177.150.027129
ORF1ab/nsp2200P200LcCtcTt3737B.1.617.20.000139
ORF1ab/nsp2200P200LcCtcTt3333AY.430.000146
ORF1ab/nsp2200P200LcCtcTt3131P.1.40.030273
ORF1ab/nsp2200P200LcCtcTt2929AY.250.000174
ORF1ab/nsp2200P200LcCtcTt2727B.1.4290.000635
ORF1ab/nsp2200P200LcCtcTt2323B.10.000211
ORF1ab/nsp2200P200LcCtcTt2222AY.240.009483
ORF1ab/nsp2200P200LcCtcTt2121AY.1030.00013
ORF1ab/nsp2200P200LcCtcTt1515AY.370.004741
ORF1ab/nsp2200P200LcCtcTt1313B.1.360.001897
ORF1ab/nsp2200P200LcCtcTt1212B.1.1600.000374
ORF1ab/nsp2200P200LcCtcTt1212B.1.5260.000282
ORF1ab/nsp2200P200LcCtcTt1010AY.420.000402
ORF1ab/nsp2200P200LcCtcTt99AY.200.00035
ORF1ab/nsp2200P200LcCtcTt99B.1.1.10.00294
ORF1ab/nsp2200P200LcCtcTt99B.1.1.2310.027864
ORF1ab/nsp2200P200LcCtcTt99B.1.1.5190.000357
ORF1ab/nsp2200P200LcCtcTt88AY.1170.000676
ORF1ab/nsp2200P200LcCtcTt88AY.330.000534
ORF1ab/nsp2200P200LcCtcTt88AY.98.10.000387
ORF1ab/nsp2200P200LcCtcTt77AY.1020.000186
ORF1ab/nsp2200P200LcCtcTt77B.1.10.000127
ORF1ab/nsp2200P200LcCtcTt66AY.1190.000212
ORF1ab/nsp2200P200LcCtcTt66AY.460.000624
ORF1ab/nsp2200P200LcCtcTt55AY.590.002648
ORF1ab/nsp2200P200LcCtcTt55B.1.1770.000066
ORF1ab/nsp2200P200LcCtcTt55B.1.2210.000355
ORF1ab/nsp2200P200LcCtcTt55B.1.466.20.001956
ORF1ab/nsp2200P200LcCtcTt55B.1.5750.001517
ORF1ab/nsp2200P200LcCtcTt55B.1.6210.000443
ORF1ab/nsp2200P200LcCtcTt55C.10.011962
ORF1ab/nsp2200P200LcCtcTt55C.370.00058
ORF1ab/nsp2200P200LcCtcTt44AY.260.000113
ORF1ab/nsp2200P200LcCtcTt44AY.470.000124
ORF1ab/nsp2200P200LcCtcTt44B.1.2100.008529
ORF1ab/nsp2200P200LcCtcTt44B.1.4710.010929
ORF1ab/nsp2200P200LcCtcTt44B.1.5960.000349
ORF1ab/nsp2200P200LcCtcTt44P.1.140.000191
ORF1ab/nsp2200P200LcCtcTt33A.2.50.001497
ORF1ab/nsp2200P200LcCtcTt33AY.1180.000188
ORF1ab/nsp2200P200LcCtcTt33AY.920.000862
ORF1ab/nsp2200P200LcCtcTt33B.1.1.4340.001046
ORF1ab/nsp2200P200LcCtcTt33B.1.1.700.001023
ORF1ab/nsp2200P200LcCtcTt33B.1.177.460.002755
ORF1ab/nsp2200P200LcCtcTt33B.1.2340.000396
ORF1ab/nsp2200P200LcCtcTt33B.1.4000.001287
ORF1ab/nsp2200P200LcCtcTt33R.10.00027
ORF1ab/nsp2200P200LcCtcTt22A.20.001324
ORF1ab/nsp2200P200LcCtcTt22AY.1060.00067
ORF1ab/nsp2200P200LcCtcTt22AY.4.20.000043
ORF1ab/nsp2200P200LcCtcTt22AY.4.30.001684
ORF1ab/nsp2200P200LcCtcTt22AY.46.30.001867
ORF1ab/nsp2200P200LcCtcTt22AY.50.000041
ORF1ab/nsp2200P200LcCtcTt22AY.650.001066
ORF1ab/nsp2200P200LcCtcTt22AY.7.10.000225
ORF1ab/nsp2200P200LcCtcTt22AY.750.000112
ORF1ab/nsp2200P200LcCtcTt22AY.760.009662
ORF1ab/nsp2200P200LcCtcTt22AY.9.20.000073
ORF1ab/nsp2200P200LcCtcTt22AY.99.20.000184
ORF1ab/nsp2200P200LcCtcTt22B0.000256
ORF1ab/nsp2200P200LcCtcTt22B.1.1.280.000622
ORF1ab/nsp2200P200LcCtcTt22B.1.177.860.000367
ORF1ab/nsp2200P200LcCtcTt22B.1.2430.000139
ORF1ab/nsp2200P200LcCtcTt22B.1.2580.000133
ORF1ab/nsp2200P200LcCtcTt22B.1.4270.000101
ORF1ab/nsp2200P200LcCtcTt22B.1.438.10.000215
ORF1ab/nsp2200P200LcCtcTt22B.1.5030.004975
ORF1ab/nsp2200P200LcCtcTt22B.1.5170.000854
ORF1ab/nsp2200P200LcCtcTt22B.1.6370.000146
ORF1ab/nsp2200P200LcCtcTt22P.30.00319
ORF1ab/nsp2200P200LcCtcTt22Q.70.002222
ORF1ab/nsp2200P200LcCtcTt11A.10.000282
ORF1ab/nsp2200P200LcCtcTt11A.250.018182
ORF1ab/nsp2200P200LcCtcTt11A.270.001656
ORF1ab/nsp2200P200LcCtcTt11AU.20.002421
ORF1ab/nsp2200P200LcCtcTt11AY.100.00053
ORF1ab/nsp2200P200LcCtcTt11AY.1000.000046
ORF1ab/nsp2200P200LcCtcTt11AY.1130.000142
ORF1ab/nsp2200P200LcCtcTt11AY.160.00038
ORF1ab/nsp2200P200LcCtcTt11AY.30.00001
ORF1ab/nsp2200P200LcCtcTt11AY.300.000396
ORF1ab/nsp2200P200LcCtcTt11AY.4.2.10.000149
ORF1ab/nsp2200P200LcCtcTt11AY.450.000122
ORF1ab/nsp2200P200LcCtcTt11AY.46.10.001027
ORF1ab/nsp2200P200LcCtcTt11AY.60.000041
ORF1ab/nsp2200P200LcCtcTt11AY.700.000209
ORF1ab/nsp2200P200LcCtcTt11AY.90.000068
ORF1ab/nsp2200P200LcCtcTt11AY.9.10.000084
ORF1ab/nsp2200P200LcCtcTt11AZ.30.00152
ORF1ab/nsp2200P200LcCtcTt11B.1.1.1480.008772
ORF1ab/nsp2200P200LcCtcTt11B.1.1.2140.000055
ORF1ab/nsp2200P200LcCtcTt11B.1.1.3030.002762
ORF1ab/nsp2200P200LcCtcTt11B.1.1.3060.000438
ORF1ab/nsp2200P200LcCtcTt11B.1.1.330.000421
ORF1ab/nsp2200P200LcCtcTt11B.1.1.3890.006061
ORF1ab/nsp2200P200LcCtcTt11B.1.1.4090.002833
ORF1ab/nsp2200P200LcCtcTt11B.1.177.210.000076
ORF1ab/nsp2200P200LcCtcTt11B.1.177.620.001192
ORF1ab/nsp2200P200LcCtcTt11B.1.177.730.000566
ORF1ab/nsp2200P200LcCtcTt11B.1.258.170.000104
ORF1ab/nsp2200P200LcCtcTt11B.1.2790.000514
ORF1ab/nsp2200P200LcCtcTt11B.1.351.30.000876
ORF1ab/nsp2200P200LcCtcTt11B.1.3670.000792
ORF1ab/nsp2200P200LcCtcTt11B.1.4150.014286
ORF1ab/nsp2200P200LcCtcTt11B.1.4250.002994
ORF1ab/nsp2200P200LcCtcTt11B.1.4990.00105
ORF1ab/nsp2200P200LcCtcTt11B.1.5250.000113
ORF1ab/nsp2200P200LcCtcTt11B.1.5950.000261
ORF1ab/nsp2200P200LcCtcTt11B.420.033333
ORF1ab/nsp2200P200LcCtcTt11B.570.015152
ORF1ab/nsp2200P200LcCtcTt11C.270.018519
ORF1ab/nsp2200P200LcCtcTt11P.1.120.000484
ORF1ab/nsp2200P200LcCtcTt11P.1.160.000374
ORF1ab/nsp2200P200LcCtcTt11P.20.000187
ORF1ab/nsp2200P200LcCtcTt11Q.10.000126
ORF1ab/nsp2200P200LcCtcTt11Q.30.000145
ORF1ab/nsp2200P200LcCtcTt11Q.80.000165

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.