CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 529

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/nsp2529F529LF709LnonsynTttCtt2041750.8578432390-2392
ORF1ab/nsp2529F529LF709LnonsynttTttA204190.09313732390-2392
ORF1ab/nsp2529F529LF709LnonsynttTttG20480.03921572390-2392
ORF1ab/nsp2529F529LF709LnonsynTtTCtA20420.009803922390-2392
ORF1ab/nsp2529F529delF709deldelTTT---747412390-2392
ORF1ab/nsp2529F529VF709VnonsynTttGtt626212390-2392
ORF1ab/nsp2529F529FF709FsynttTttC585812390-2392
ORF1ab/nsp2529F529IF709InonsynTttAtt353512390-2392
ORF1ab/nsp2529F529SF709SnonsyntTttCt17140.8235292390-2392
ORF1ab/nsp2529F529SF709SnonsynTTtAGt1710.05882352390-2392
ORF1ab/nsp2529F529SF709SnonsyntTTtCG1710.05882352390-2392
ORF1ab/nsp2529F529SF709SnonsyntTTtCC1710.05882352390-2392
ORF1ab/nsp2529F529YF709YnonsyntTttAt131312390-2392
ORF1ab/nsp2529F529CF709CnonsyntTttGt12110.9166672390-2392
ORF1ab/nsp2529F529del1F709del1delTtt-tt12110.9166672390-2392
ORF1ab/nsp2529F529del1F709del1delTTt-Ct1210.08333332390-2392
ORF1ab/nsp2529F529CF709CnonsyntTTtGC1210.08333332390-2392
ORF1ab/nsp2529F529XF709XnonsyntTTtAA1050.52390-2392
ORF1ab/nsp2529F529XF709XnonsyntTTtGA1050.52390-2392
ORF1ab/nsp2529F529del2F709del2delTTT--A520.42390-2392
ORF1ab/nsp2529F529del2F709del2deltTTt--520.42390-2392
ORF1ab/nsp2529F529del2F709del2delTTT--C510.22390-2392
ORF1ab/nsp2529F529TF709TnonsynTTtACt2212390-2392
ORF1ab/nsp2529F529NF709NnonsynTTtAAt1112390-2392
ORF1ab/nsp2529F529HF709HnonsynTTtCAt1112390-2392
ORF1ab/nsp2529F529PF709PnonsynTTtCCt1112390-2392
ORF1ab/nsp2529F529RF709RnonsynTTtCGt1112390-2392

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/nsp2529F529LTttCtt175204All0.000033
ORF1ab/nsp2529F529LttTttA19204All0.000004
ORF1ab/nsp2529F529LttTttG8204All0.000002
ORF1ab/nsp2529F529LTtTCtA2204All0
ORF1ab/nsp2529F529delTTT---7474All0.000014
ORF1ab/nsp2529F529VTttGtt6262All0.000012
ORF1ab/nsp2529F529FttTttC5858All0.000011
ORF1ab/nsp2529F529ITttAtt3535All0.000007
ORF1ab/nsp2529F529LTttCtt2727AY.30.000269
ORF1ab/nsp2529F529LTttCtt1320B.1.1.70.000012
ORF1ab/nsp2529F529LttTttA520B.1.1.70.000004
ORF1ab/nsp2529F529LttTttG220B.1.1.70.000002
ORF1ab/nsp2529F529VTttGtt1818AY.980.001422
ORF1ab/nsp2529F529StTttCt1417All0.000003
ORF1ab/nsp2529F529StTTtCC117All0
ORF1ab/nsp2529F529StTTtCG117All0
ORF1ab/nsp2529F529STTtAGt117All0
ORF1ab/nsp2529F529VTttGtt1717B.1.1.70.000015
ORF1ab/nsp2529F529delTTT---1616B.1.1.70.000014
ORF1ab/nsp2529F529LTttCtt1415AY.40.000022
ORF1ab/nsp2529F529LttTttA115AY.40.000002
ORF1ab/nsp2529F529ITttAtt1414AY.99.20.00129
ORF1ab/nsp2529F529FttTttC1414B.1.1.3300.875
ORF1ab/nsp2529F529YtTttAt1313All0.000002
ORF1ab/nsp2529F529del1Ttt-tt1112All0.000002
ORF1ab/nsp2529F529CtTttGt1112All0.000002
ORF1ab/nsp2529F529CtTTtGC112All0
ORF1ab/nsp2529F529del1TTt-Ct112All0
ORF1ab/nsp2529F529LTttCtt1212B.1.258.140.011765
ORF1ab/nsp2529F529LTttCtt711B.1.20.000062
ORF1ab/nsp2529F529LttTttA411B.1.20.000035
ORF1ab/nsp2529F529XtTTtAA510All0.000001
ORF1ab/nsp2529F529XtTTtGA510All0.000001
ORF1ab/nsp2529F529FttTttC88AY.40.000012
ORF1ab/nsp2529F529XtTTtGA48B.1.20.000035
ORF1ab/nsp2529F529XtTTtAA48B.1.20.000035
ORF1ab/nsp2529F529LTttCtt77AY.200.000272
ORF1ab/nsp2529F529LTttCtt77B.10.000064
ORF1ab/nsp2529F529FttTttC77B.1.1.70.000006
ORF1ab/nsp2529F529ITttAtt77B.1.1.70.000006
ORF1ab/nsp2529F529LTttCtt77B.1.4290.000165
ORF1ab/nsp2529F529LTttCtt77P.10.00011
ORF1ab/nsp2529F529delTTT---660.333333
ORF1ab/nsp2529F529LTttCtt66AY.1030.000037
ORF1ab/nsp2529F529VTttGtt66AY.40.000009
ORF1ab/nsp2529F529delTTT---66B.10.000055
ORF1ab/nsp2529F529YtTttAt66B.1.1.70.000005
ORF1ab/nsp2529F529LTttCtt56B.1.617.20.000019
ORF1ab/nsp2529F529LttTttA16B.1.617.20.000004
ORF1ab/nsp2529F529del2tTTt--25All0
ORF1ab/nsp2529F529del2TTT--A25All0
ORF1ab/nsp2529F529del2TTT--C15All0
ORF1ab/nsp2529F529LTttCtt55AY.430.000022
ORF1ab/nsp2529F529FttTttC55B.1.1.1700.006234
ORF1ab/nsp2529F529LTttCtt55B.1.1.4340.001743
ORF1ab/nsp2529F529YtTttAt55B.1.20.000044
ORF1ab/nsp2529F529LTttCtt55B.1.2580.000333
ORF1ab/nsp2529F529LttTttA44AY.1000.000184
ORF1ab/nsp2529F529VTttGtt44AY.250.000024
ORF1ab/nsp2529F529LTttCtt44AY.3.10.000341
ORF1ab/nsp2529F529ITttAtt44AY.40.000006
ORF1ab/nsp2529F529LTttCtt44B.1.10.000073
ORF1ab/nsp2529F529CtTttGt44B.1.20.000035
ORF1ab/nsp2529F529LTtTCtA230.111111
ORF1ab/nsp2529F529LttTttG130.055556
ORF1ab/nsp2529F529LttTttG33AY.1180.000188
ORF1ab/nsp2529F529VTttGtt33AY.30.00003
ORF1ab/nsp2529F529LTttCtt33AY.440.000018
ORF1ab/nsp2529F529VTttGtt33AY.740.000347
ORF1ab/nsp2529F529FttTttC33B.10.000027
ORF1ab/nsp2529F529delTTT---33B.1.1.330.001263
ORF1ab/nsp2529F529StTttCt23B.1.1.70.000002
ORF1ab/nsp2529F529STTtAGt13B.1.1.70.000001
ORF1ab/nsp2529F529del1Ttt-tt23B.1.20.000018
ORF1ab/nsp2529F529del1TTt-Ct13B.1.20.000009
ORF1ab/nsp2529F529LTttCtt33B.1.5260.000071
ORF1ab/nsp2529F529delTTT---33B.1.617.20.000011
ORF1ab/nsp2529F529del2TTT--A23B.1.617.20.000008
ORF1ab/nsp2529F529del2TTT--C13B.1.617.20.000004
ORF1ab/nsp2529F529ITttAtt33P.10.000047
ORF1ab/nsp2529F529TTTtACt22All0
ORF1ab/nsp2529F529LTttCtt22AY.120.000632
ORF1ab/nsp2529F529StTttCt22AY.250.000012
ORF1ab/nsp2529F529LTttCtt22AY.250.000012
ORF1ab/nsp2529F529LTttCtt22AY.390.000049
ORF1ab/nsp2529F529delTTT---22AY.430.000009
ORF1ab/nsp2529F529del2tTTt--22AY.430.000009
ORF1ab/nsp2529F529FttTttC22AY.470.000062
ORF1ab/nsp2529F529delTTT---22AY.990.002099
ORF1ab/nsp2529F529StTttCt22B.1.10.000036
ORF1ab/nsp2529F529delTTT---22B.1.10.000036
ORF1ab/nsp2529F529delTTT---22B.1.1.3480.001592
ORF1ab/nsp2529F529CtTttGt12B.1.177.530.002392
ORF1ab/nsp2529F529CtTTtGC12B.1.177.530.002392
ORF1ab/nsp2529F529FttTttC22B.1.20.000018
ORF1ab/nsp2529F529XtTTtAA12B.1.2340.000132
ORF1ab/nsp2529F529XtTTtGA12B.1.2340.000132
ORF1ab/nsp2529F529delTTT---22B.1.4240.016129
ORF1ab/nsp2529F529delTTT---22B.1.4290.000047
ORF1ab/nsp2529F529FttTttC22B.1.5260.000047
ORF1ab/nsp2529F529delTTT---22B.1.617.10.000258
ORF1ab/nsp2529F529FttTttC22B.1.617.20.000008
ORF1ab/nsp2529F529LTttCtt22B.1.6210.000177
ORF1ab/nsp2529F529delTTT---22N.60.014184
ORF1ab/nsp2529F529LTttCtt22P.1.140.000096
ORF1ab/nsp2529F529ITttAtt110.055556
ORF1ab/nsp2529F529LTttCtt11A.2.50.000499
ORF1ab/nsp2529F529RTTtCGt11All0
ORF1ab/nsp2529F529NTTtAAt11All0
ORF1ab/nsp2529F529HTTtCAt11All0
ORF1ab/nsp2529F529PTTtCCt11All0
ORF1ab/nsp2529F529YtTttAt11AY.1030.000006
ORF1ab/nsp2529F529VTttGtt11AY.1030.000006
ORF1ab/nsp2529F529LttTttA11AY.1040.001984
ORF1ab/nsp2529F529delTTT---11AY.1080.001103
ORF1ab/nsp2529F529LTttCtt11AY.1100.000113
ORF1ab/nsp2529F529delTTT---11AY.1130.000142
ORF1ab/nsp2529F529FttTttC11AY.1140.000231
ORF1ab/nsp2529F529LTttCtt11AY.1170.000085
ORF1ab/nsp2529F529delTTT---11AY.1170.000085
ORF1ab/nsp2529F529FttTttC11AY.140.000088
ORF1ab/nsp2529F529LTttCtt11AY.230.00007
ORF1ab/nsp2529F529FttTttC11AY.230.00007
ORF1ab/nsp2529F529del1Ttt-tt11AY.250.000006
ORF1ab/nsp2529F529delTTT---11AY.260.000028
ORF1ab/nsp2529F529LTttCtt11AY.260.000028
ORF1ab/nsp2529F529delTTT---11AY.29.10.000221
ORF1ab/nsp2529F529LTttCtt11AY.330.000067
ORF1ab/nsp2529F529delTTT---11AY.40.000002
ORF1ab/nsp2529F529del1Ttt-tt11AY.40.000002
ORF1ab/nsp2529F529LttTttG11AY.4.20.000022
ORF1ab/nsp2529F529VTttGtt11AY.4.2.10.000149
ORF1ab/nsp2529F529ITttAtt11AY.4.50.000107
ORF1ab/nsp2529F529VTttGtt11AY.4.50.000107
ORF1ab/nsp2529F529FttTttC11AY.430.000004
ORF1ab/nsp2529F529del1Ttt-tt11AY.440.000006
ORF1ab/nsp2529F529delTTT---11AY.440.000006
ORF1ab/nsp2529F529FttTttC11AY.440.000006
ORF1ab/nsp2529F529LTttCtt11AY.450.000122
ORF1ab/nsp2529F529VTttGtt11AY.460.000104
ORF1ab/nsp2529F529LTttCtt11AY.46.10.001027
ORF1ab/nsp2529F529delTTT---11AY.46.60.000072
ORF1ab/nsp2529F529LTttCtt11AY.50.000021
ORF1ab/nsp2529F529ITttAtt11AY.50.000021
ORF1ab/nsp2529F529LTttCtt11AY.5.40.000277
ORF1ab/nsp2529F529StTttCt11AY.520.000814
ORF1ab/nsp2529F529LTttCtt11AY.60.000041
ORF1ab/nsp2529F529delTTT---11AY.620.000436
ORF1ab/nsp2529F529FttTttC11AY.650.000533
ORF1ab/nsp2529F529LTttCtt11AY.710.000475
ORF1ab/nsp2529F529LTttCtt11AY.730.000665
ORF1ab/nsp2529F529delTTT---11AY.750.000056
ORF1ab/nsp2529F529delTTT---11AY.840.000437
ORF1ab/nsp2529F529VTttGtt11AY.840.000437
ORF1ab/nsp2529F529del1Ttt-tt11AY.90.000068
ORF1ab/nsp2529F529LTttCtt11AY.9.20.000037
ORF1ab/nsp2529F529delTTT---11AY.98.10.000048
ORF1ab/nsp2529F529TTTtACt11B0.000128
ORF1ab/nsp2529F529LTttCtt11B0.000128
ORF1ab/nsp2529F529del1Ttt-tt11B.10.000009
ORF1ab/nsp2529F529ITttAtt11B.10.000009
ORF1ab/nsp2529F529FttTttC11B.1.10.000018
ORF1ab/nsp2529F529del1Ttt-tt11B.1.10.000018
ORF1ab/nsp2529F529VTttGtt11B.1.10.000018
ORF1ab/nsp2529F529CtTttGt11B.1.10.000018
ORF1ab/nsp2529F529ITttAtt11B.1.10.000018
ORF1ab/nsp2529F529delTTT---11B.1.1.1130.006993
ORF1ab/nsp2529F529del1Ttt-tt11B.1.1.120.007463
ORF1ab/nsp2529F529delTTT---11B.1.1.1390.022727
ORF1ab/nsp2529F529LttTttA11B.1.1.2140.000055
ORF1ab/nsp2529F529VTttGtt11B.1.1.2140.000055
ORF1ab/nsp2529F529LttTttA11B.1.1.2220.000204
ORF1ab/nsp2529F529StTTtCC11B.1.1.2790.001121
ORF1ab/nsp2529F529VTttGtt11B.1.1.2940.001266
ORF1ab/nsp2529F529VTttGtt11B.1.1.3000.010753
ORF1ab/nsp2529F529FttTttC11B.1.1.3180.000302
ORF1ab/nsp2529F529LTttCtt11B.1.1.330.000421
ORF1ab/nsp2529F529ITttAtt11B.1.1.3540.004386
ORF1ab/nsp2529F529CtTttGt11B.1.1.370.000193
ORF1ab/nsp2529F529LTttCtt11B.1.1.3970.002252
ORF1ab/nsp2529F529LttTttG11B.1.1.3980.003226
ORF1ab/nsp2529F529delTTT---11B.1.1.4160.000905
ORF1ab/nsp2529F529delTTT---11B.1.1.4480.002033
ORF1ab/nsp2529F529NTTtAAt11B.1.1.70.000001
ORF1ab/nsp2529F529HTTtCAt11B.1.1.70.000001
ORF1ab/nsp2529F529CtTttGt11B.1.1.70.000001
ORF1ab/nsp2529F529TTTtACt11B.1.1.70.000001
ORF1ab/nsp2529F529RTTtCGt11B.1.1.70.000001
ORF1ab/nsp2529F529del1Ttt-tt11B.1.1.70.000001
ORF1ab/nsp2529F529PTTtCCt11B.1.1.70.000001
ORF1ab/nsp2529F529StTttCt11B.1.1600.000031
ORF1ab/nsp2529F529StTttCt11B.1.160.140.002119
ORF1ab/nsp2529F529StTttCt11B.1.160.260.002421
ORF1ab/nsp2529F529FttTttC11B.1.1770.000013
ORF1ab/nsp2529F529CtTttGt11B.1.1770.000013
ORF1ab/nsp2529F529FttTttC11B.1.177.530.002392
ORF1ab/nsp2529F529FttTttC11B.1.177.540.000606
ORF1ab/nsp2529F529delTTT---11B.1.1790.003759
ORF1ab/nsp2529F529StTTtCG11B.1.20.000009
ORF1ab/nsp2529F529LTttCtt11B.1.214.20.0006
ORF1ab/nsp2529F529StTttCt11B.1.214.20.0006
ORF1ab/nsp2529F529CtTttGt11B.1.2340.000132
ORF1ab/nsp2529F529LttTttA11B.1.2340.000132
ORF1ab/nsp2529F529YtTttAt11B.1.2340.000132
ORF1ab/nsp2529F529delTTT---11B.1.2580.000067
ORF1ab/nsp2529F529ITttAtt11B.1.351.50.0006
ORF1ab/nsp2529F529LTttCtt11B.1.36.170.000494
ORF1ab/nsp2529F529delTTT---11B.1.416.10.001563
ORF1ab/nsp2529F529VTttGtt11B.1.4250.002994
ORF1ab/nsp2529F529LTttCtt11B.1.4480.002625
ORF1ab/nsp2529F529CtTttGt11B.1.4970.000315
ORF1ab/nsp2529F529LTttCtt11B.1.5030.002488
ORF1ab/nsp2529F529delTTT---11B.1.5610.000397
ORF1ab/nsp2529F529LTttCtt11B.1.5750.000303
ORF1ab/nsp2529F529StTttCt11B.1.5960.000087
ORF1ab/nsp2529F529VTttGtt11B.1.617.20.000004
ORF1ab/nsp2529F529StTttCt11B.1.617.20.000004
ORF1ab/nsp2529F529delTTT---11B.1.6210.000089
ORF1ab/nsp2529F529LTttCtt11B.1.6280.000352
ORF1ab/nsp2529F529LTttCtt11B.3.10.001658
ORF1ab/nsp2529F529delTTT---11B.570.015152
ORF1ab/nsp2529F529del1Ttt-tt11D.20.000075
ORF1ab/nsp2529F529FttTttC11D.20.000075
ORF1ab/nsp2529F529StTttCt11D.20.000075
ORF1ab/nsp2529F529FttTttC11P.10.000016
ORF1ab/nsp2529F529delTTT---11P.10.000016
ORF1ab/nsp2529F529delTTT---11P.20.000187

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.