CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 509

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/nsp2509C509GC689GnonsynTgtGgt28028012330-2332
ORF1ab/nsp2509C509YC689YnonsyntGttAt1081070.9907412330-2332
ORF1ab/nsp2509C509YC689YnonsyntGTtAC10810.009259262330-2332
ORF1ab/nsp2509C509delC689deldelTGT---737312330-2332
ORF1ab/nsp2509C509CC689CsyntgTtgC727212330-2332
ORF1ab/nsp2509C509FC689FnonsyntGttTt343412330-2332
ORF1ab/nsp2509C509SC689SnonsynTgtAgt19100.5263162330-2332
ORF1ab/nsp2509C509SC689SnonsyntGttCt1960.3157892330-2332
ORF1ab/nsp2509C509SC689SnonsyntGTtCC1920.1052632330-2332
ORF1ab/nsp2509C509SC689SnonsyntGTtCG1910.05263162330-2332
ORF1ab/nsp2509C509RC689RnonsynTgtCgt18170.9444442330-2332
ORF1ab/nsp2509C509RC689RnonsynTgTCgA1810.05555562330-2332
ORF1ab/nsp2509C509WC689WnonsyntgTtgG121212330-2332
ORF1ab/nsp2509C509del1C689del1deltGtt-t630.52330-2332
ORF1ab/nsp2509C509del1C689del1delTGt-At610.1666672330-2332
ORF1ab/nsp2509C509del1C689del1delTGTAA-610.1666672330-2332
ORF1ab/nsp2509C509del1C689del1delTgt-gt610.1666672330-2332
ORF1ab/nsp2509C509HC689HnonsynTGTCAC2212330-2332
ORF1ab/nsp2509C509XC689XnonsyntGTtAA2212330-2332
ORF1ab/nsp2509C509DC689DnonsynTGtGAt1112330-2332
ORF1ab/nsp2509C509KC689KnonsynTGTAAA1112330-2332
ORF1ab/nsp2509C509VC689VnonsynTGTGTA1112330-2332
ORF1ab/nsp2509C509del2C689del2delTGt--t1112330-2332
ORF1ab/nsp2509C509NC689NnonsynTGTAAC1112330-2332

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/nsp2509C509GTgtGgt280280All0.000054
ORF1ab/nsp2509C509GTgtGgt267267B.1.5740.574194
ORF1ab/nsp2509C509YtGttAt107108All0.00002
ORF1ab/nsp2509C509YtGTtAC1108All0
ORF1ab/nsp2509C509delTGT---7373All0.000014
ORF1ab/nsp2509C509CtgTtgC7272All0.000014
ORF1ab/nsp2509C509FtGttTt3434All0.000007
ORF1ab/nsp2509C509CtgTtgC2929B.1.20.000255
ORF1ab/nsp2509C509YtGttAt2626B.1.2430.001809
ORF1ab/nsp2509C509delTGT---2020B.1.1.70.000018
ORF1ab/nsp2509C509STgtAgt1019All0.000002
ORF1ab/nsp2509C509StGttCt619All0.000001
ORF1ab/nsp2509C509StGTtCC219All0
ORF1ab/nsp2509C509StGTtCG119All0
ORF1ab/nsp2509C509RTgtCgt1718All0.000003
ORF1ab/nsp2509C509RTgTCgA118All0
ORF1ab/nsp2509C509WtgTtgG1212All0.000002
ORF1ab/nsp2509C509CtgTtgC99B.10.000082
ORF1ab/nsp2509C509YtGttAt88AY.40.000012
ORF1ab/nsp2509C509YtGttAt88B.1.1.70.000007
ORF1ab/nsp2509C509delTGT---660.333333
ORF1ab/nsp2509C509del1tGtt-t36All0.000001
ORF1ab/nsp2509C509del1TGTAA-16All0
ORF1ab/nsp2509C509del1Tgt-gt16All0
ORF1ab/nsp2509C509del1TGt-At16All0
ORF1ab/nsp2509C509delTGT---66B.10.000055
ORF1ab/nsp2509C509GTgtGgt66B.10.000055
ORF1ab/nsp2509C509YtGttAt66B.10.000055
ORF1ab/nsp2509C509CtgTtgC55AY.1030.000031
ORF1ab/nsp2509C509CtgTtgC55B.1.617.20.000019
ORF1ab/nsp2509C509YtGttAt45B.1.617.20.000015
ORF1ab/nsp2509C509YtGTtAC15B.1.617.20.000004
ORF1ab/nsp2509C509FtGttTt44AY.4.40.001637
ORF1ab/nsp2509C509YtGttAt44AY.430.000018
ORF1ab/nsp2509C509RTgtCgt34AY.440.000018
ORF1ab/nsp2509C509RTgTCgA14AY.440.000006
ORF1ab/nsp2509C509CtgTtgC44AY.470.000124
ORF1ab/nsp2509C509StGttCt24B.10.000018
ORF1ab/nsp2509C509STgtAgt24B.10.000018
ORF1ab/nsp2509C509YtGttAt44B.1.3510.000119
ORF1ab/nsp2509C509delTGT---44B.1.617.20.000015
ORF1ab/nsp2509C509FtGttTt44B.1.617.20.000015
ORF1ab/nsp2509C509YtGttAt33AY.260.000085
ORF1ab/nsp2509C509delTGT---33AY.430.000013
ORF1ab/nsp2509C509FtGttTt33AY.440.000018
ORF1ab/nsp2509C509YtGttAt33AY.98.10.000145
ORF1ab/nsp2509C509delTGT---33B.1.1.330.001263
ORF1ab/nsp2509C509YtGttAt33B.1.20.000026
ORF1ab/nsp2509C509WtgTtgG33B.1.2400.000647
ORF1ab/nsp2509C509YtGttAt33B.1.4680.017143
ORF1ab/nsp2509C509YtGttAt33B.1.5950.000783
ORF1ab/nsp2509C509XtGTtAA22All0
ORF1ab/nsp2509C509HTGTCAC22All0
ORF1ab/nsp2509C509YtGttAt22AY.1030.000012
ORF1ab/nsp2509C509CtgTtgC22AY.250.000012
ORF1ab/nsp2509C509FtGttTt22AY.250.000012
ORF1ab/nsp2509C509YtGttAt22AY.30.00002
ORF1ab/nsp2509C509GTgtGgt22AY.40.000003
ORF1ab/nsp2509C509CtgTtgC22AY.40.000003
ORF1ab/nsp2509C509YtGttAt22AY.440.000012
ORF1ab/nsp2509C509CtgTtgC22AY.940.000885
ORF1ab/nsp2509C509delTGT---22AY.990.002099
ORF1ab/nsp2509C509RTgtCgt22B.10.000018
ORF1ab/nsp2509C509FtGttTt22B.10.000018
ORF1ab/nsp2509C509delTGT---22B.1.10.000036
ORF1ab/nsp2509C509delTGT---22B.1.1.3480.001592
ORF1ab/nsp2509C509WtgTtgG22B.1.1.70.000002
ORF1ab/nsp2509C509StGttCt12B.1.1.70.000001
ORF1ab/nsp2509C509STgtAgt12B.1.1.70.000001
ORF1ab/nsp2509C509CtgTtgC22B.1.1770.000026
ORF1ab/nsp2509C509FtGttTt22B.1.20.000018
ORF1ab/nsp2509C509RTgtCgt22B.1.20.000018
ORF1ab/nsp2509C509YtGttAt22B.1.2790.001027
ORF1ab/nsp2509C509YtGttAt22B.1.360.000292
ORF1ab/nsp2509C509delTGT---22B.1.4240.016129
ORF1ab/nsp2509C509delTGT---22B.1.4290.000047
ORF1ab/nsp2509C509YtGttAt22B.1.4590.008163
ORF1ab/nsp2509C509YtGttAt22B.1.5240.002813
ORF1ab/nsp2509C509STgtAgt12B.1.617.20.000004
ORF1ab/nsp2509C509StGTtCC12B.1.617.20.000004
ORF1ab/nsp2509C509del1tGtt-t22B.1.6270.00404
ORF1ab/nsp2509C509delTGT---22N.60.014184
ORF1ab/nsp2509C509FtGttTt11A.10.000282
ORF1ab/nsp2509C509FtGttTt11A.20.000662
ORF1ab/nsp2509C509STgtAgt11A.2.40.003367
ORF1ab/nsp2509C509YtGttAt11A.290.005319
ORF1ab/nsp2509C509VTGTGTA11All0
ORF1ab/nsp2509C509KTGTAAA11All0
ORF1ab/nsp2509C509del2TGt--t11All0
ORF1ab/nsp2509C509NTGTAAC11All0
ORF1ab/nsp2509C509DTGtGAt11All0
ORF1ab/nsp2509C509YtGttAt11AY.1020.000027
ORF1ab/nsp2509C509STgtAgt11AY.1030.000006
ORF1ab/nsp2509C509del1TGTAA-11AY.1030.000006
ORF1ab/nsp2509C509delTGT---11AY.1030.000006
ORF1ab/nsp2509C509delTGT---11AY.1080.001103
ORF1ab/nsp2509C509WtgTtgG11AY.1130.000142
ORF1ab/nsp2509C509StGTtCG11AY.1130.000142
ORF1ab/nsp2509C509RTgtCgt11AY.1140.000231
ORF1ab/nsp2509C509GTgtGgt11AY.1170.000085
ORF1ab/nsp2509C509YtGttAt11AY.1180.000063
ORF1ab/nsp2509C509FtGttTt11AY.1190.000035
ORF1ab/nsp2509C509YtGttAt11AY.1190.000035
ORF1ab/nsp2509C509XtGTtAA11AY.120.10.000321
ORF1ab/nsp2509C509CtgTtgC11AY.130.000161
ORF1ab/nsp2509C509RTgtCgt11AY.230.00007
ORF1ab/nsp2509C509WtgTtgG11AY.250.000006
ORF1ab/nsp2509C509YtGttAt11AY.250.000006
ORF1ab/nsp2509C509YtGttAt11AY.290.000016
ORF1ab/nsp2509C509delTGT---11AY.29.10.000221
ORF1ab/nsp2509C509delTGT---11AY.30.00001
ORF1ab/nsp2509C509RTgtCgt11AY.30.00001
ORF1ab/nsp2509C509WtgTtgG11AY.330.000067
ORF1ab/nsp2509C509delTGT---11AY.390.000025
ORF1ab/nsp2509C509StGttCt11AY.390.000025
ORF1ab/nsp2509C509FtGttTt11AY.40.000002
ORF1ab/nsp2509C509delTGT---11AY.40.000002
ORF1ab/nsp2509C509RTgtCgt11AY.420.00004
ORF1ab/nsp2509C509YtGttAt11AY.420.00004
ORF1ab/nsp2509C509WtgTtgG11AY.430.000004
ORF1ab/nsp2509C509RTgtCgt11AY.430.000004
ORF1ab/nsp2509C509FtGttTt11AY.430.000004
ORF1ab/nsp2509C509GTgtGgt11AY.440.000006
ORF1ab/nsp2509C509CtgTtgC11AY.440.000006
ORF1ab/nsp2509C509delTGT---11AY.440.000006
ORF1ab/nsp2509C509HTGTCAC11AY.46.60.000072
ORF1ab/nsp2509C509YtGttAt11AY.46.60.000072
ORF1ab/nsp2509C509STgtAgt11AY.480.000465
ORF1ab/nsp2509C509FtGttTt11AY.50.000021
ORF1ab/nsp2509C509YtGttAt11AY.60.000041
ORF1ab/nsp2509C509RTgtCgt11AY.60.000041
ORF1ab/nsp2509C509FtGttTt11AY.610.000105
ORF1ab/nsp2509C509delTGT---11AY.670.000464
ORF1ab/nsp2509C509StGTtCC11AY.750.000056
ORF1ab/nsp2509C509RTgtCgt11AY.750.000056
ORF1ab/nsp2509C509delTGT---11AY.840.000437
ORF1ab/nsp2509C509delTGT---11AY.9.20.000037
ORF1ab/nsp2509C509FtGttTt11AY.9.20.000037
ORF1ab/nsp2509C509StGttCt11AY.98.10.000048
ORF1ab/nsp2509C509WtgTtgG11AY.99.20.000092
ORF1ab/nsp2509C509del1TGt-At11B.10.000009
ORF1ab/nsp2509C509WtgTtgG11B.10.000009
ORF1ab/nsp2509C509FtGttTt11B.1.10.000018
ORF1ab/nsp2509C509KTGTAAA11B.1.10.000018
ORF1ab/nsp2509C509CtgTtgC11B.1.1.1700.001247
ORF1ab/nsp2509C509YtGttAt11B.1.1.2940.001266
ORF1ab/nsp2509C509delTGT---11B.1.1.4160.000905
ORF1ab/nsp2509C509CtgTtgC11B.1.1.5190.00004
ORF1ab/nsp2509C509RTgtCgt11B.1.1.5230.001563
ORF1ab/nsp2509C509delTGT---11B.1.1.5230.001563
ORF1ab/nsp2509C509DTGtGAt11B.1.1.70.000001
ORF1ab/nsp2509C509NTGTAAC11B.1.1.70.000001
ORF1ab/nsp2509C509VTGTGTA11B.1.1.70.000001
ORF1ab/nsp2509C509CtgTtgC11B.1.1.70.000001
ORF1ab/nsp2509C509del1Tgt-gt11B.1.1.70.000001
ORF1ab/nsp2509C509GTgtGgt11B.1.1.70.000001
ORF1ab/nsp2509C509FtGttTt11B.1.1.70.000001
ORF1ab/nsp2509C509YtGttAt11B.1.1600.000031
ORF1ab/nsp2509C509CtgTtgC11B.1.1600.000031
ORF1ab/nsp2509C509HTGTCAC11B.1.1600.000031
ORF1ab/nsp2509C509GTgtGgt11B.1.160.220.006757
ORF1ab/nsp2509C509RTgtCgt11B.1.1770.000013
ORF1ab/nsp2509C509YtGttAt11B.1.1770.000013
ORF1ab/nsp2509C509delTGT---11B.1.1770.000013
ORF1ab/nsp2509C509FtGttTt11B.1.1770.000013
ORF1ab/nsp2509C509YtGttAt11B.1.177.40.000211
ORF1ab/nsp2509C509STgtAgt11B.1.177.530.002392
ORF1ab/nsp2509C509CtgTtgC11B.1.177.870.000728
ORF1ab/nsp2509C509delTGT---11B.1.1790.003759
ORF1ab/nsp2509C509WtgTtgG11B.1.20.000009
ORF1ab/nsp2509C509FtGttTt11B.1.2210.000071
ORF1ab/nsp2509C509StGttCt11B.1.2580.000067
ORF1ab/nsp2509C509FtGttTt11B.1.3510.00003
ORF1ab/nsp2509C509YtGttAt11B.1.36.190.009259
ORF1ab/nsp2509C509RTgtCgt11B.1.36.290.000517
ORF1ab/nsp2509C509STgtAgt11B.1.4040.001302
ORF1ab/nsp2509C509delTGT---11B.1.416.10.001563
ORF1ab/nsp2509C509STgtAgt11B.1.4270.00005
ORF1ab/nsp2509C509CtgTtgC11B.1.4380.006536
ORF1ab/nsp2509C509YtGttAt11B.1.438.10.000107
ORF1ab/nsp2509C509CtgTtgC11B.1.5170.000427
ORF1ab/nsp2509C509FtGttTt11B.1.5250.000113
ORF1ab/nsp2509C509delTGT---11B.1.5610.000397
ORF1ab/nsp2509C509GTgtGgt11B.1.5960.000087
ORF1ab/nsp2509C509del1tGtt-t11B.1.617.20.000004
ORF1ab/nsp2509C509del2TGt--t11B.1.617.20.000004
ORF1ab/nsp2509C509XtGTtAA11B.1.617.20.000004
ORF1ab/nsp2509C509delTGT---11B.570.015152
ORF1ab/nsp2509C509CtgTtgC11C.360.000911
ORF1ab/nsp2509C509FtGttTt11C.370.000116
ORF1ab/nsp2509C509FtGttTt11D.20.000075
ORF1ab/nsp2509C509CtgTtgC11P.10.000016
ORF1ab/nsp2509C509delTGT---11P.10.000016
ORF1ab/nsp2509C509YtGttAt11P.10.000016
ORF1ab/nsp2509C509FtGttTt11P.10.000016
ORF1ab/nsp2509C509YtGttAt11P.1.120.000484
ORF1ab/nsp2509C509YtGttAt11P.1.160.000374
ORF1ab/nsp2509C509CtgTtgC11P.1.160.000374
ORF1ab/nsp2509C509delTGT---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.