CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 560

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/nsp12560V560VV4952VsyngtCgtT106610000.93808615118-15120
ORF1ab/nsp12560V560VV4952VsyngtCgtA1066540.050656715118-15120
ORF1ab/nsp12560V560VV4952VsyngtCgtG1066120.01125715118-15120
ORF1ab/nsp12560V560delV4952deldelGTC---2424115118-15120
ORF1ab/nsp12560V560AV4952AnonsyngTcgCc1414115118-15120
ORF1ab/nsp12560V560FV4952FnonsynGtcTtc1290.7515118-15120
ORF1ab/nsp12560V560FV4952FnonsynGtCTtT1230.2515118-15120
ORF1ab/nsp12560V560GV4952GnonsyngTcgGc750.71428615118-15120
ORF1ab/nsp12560V560GV4952GnonsyngTCgGG710.14285715118-15120
ORF1ab/nsp12560V560GV4952GnonsyngTCgGT710.14285715118-15120
ORF1ab/nsp12560V560IV4952InonsynGtcAtc540.815118-15120
ORF1ab/nsp12560V560IV4952InonsynGtCAtT510.215118-15120
ORF1ab/nsp12560V560del2V4952del2delGTc--c44115118-15120
ORF1ab/nsp12560V560DV4952DnonsyngTcgAc44115118-15120
ORF1ab/nsp12560V560LV4952LnonsynGtcCtc430.7515118-15120
ORF1ab/nsp12560V560del1V4952del1delGtc-tc430.7515118-15120
ORF1ab/nsp12560V560del1V4952del1delgtCgt-410.2515118-15120
ORF1ab/nsp12560V560LV4952LnonsynGtCTtA410.2515118-15120
ORF1ab/nsp12560V560MV4952MnonsynGtCAtG22115118-15120
ORF1ab/nsp12560V560CV4952CnonsynGTcTGc210.515118-15120
ORF1ab/nsp12560V560EV4952EnonsyngTCgAA210.515118-15120
ORF1ab/nsp12560V560SV4952SnonsynGTcAGc210.515118-15120
ORF1ab/nsp12560V560EV4952EnonsyngTCgAG210.515118-15120
ORF1ab/nsp12560V560CV4952CnonsynGTCTGT210.515118-15120
ORF1ab/nsp12560V560SV4952SnonsynGTcTCc210.515118-15120
ORF1ab/nsp12560V560RV4952RnonsynGTCAGG11115118-15120
ORF1ab/nsp12560V560KV4952KnonsynGTCAAG11115118-15120
ORF1ab/nsp12560V560NV4952NnonsynGTcAAc11115118-15120

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/nsp12560V560VgtCgtT10001066All0.000191
ORF1ab/nsp12560V560VgtCgtA541066All0.00001
ORF1ab/nsp12560V560VgtCgtG121066All0.000002
ORF1ab/nsp12560V560VgtCgtT159169B.1.1.70.000142
ORF1ab/nsp12560V560VgtCgtA5169B.1.1.70.000004
ORF1ab/nsp12560V560VgtCgtG5169B.1.1.70.000004
ORF1ab/nsp12560V560VgtCgtT138144AY.40.000215
ORF1ab/nsp12560V560VgtCgtA6144AY.40.000009
ORF1ab/nsp12560V560VgtCgtT121122B.1.617.20.000456
ORF1ab/nsp12560V560VgtCgtG1122B.1.617.20.000004
ORF1ab/nsp12560V560VgtCgtT8686AY.1020.00228
ORF1ab/nsp12560V560VgtCgtT5050N.50.088339
ORF1ab/nsp12560V560VgtCgtT4747B.1.4600.839286
ORF1ab/nsp12560V560VgtCgtT3535AY.430.000155
ORF1ab/nsp12560V560VgtCgtT3233B.1.20.000282
ORF1ab/nsp12560V560VgtCgtA133B.1.20.000009
ORF1ab/nsp12560V560delGTC---2424All0.000005
ORF1ab/nsp12560V560VgtCgtT2424AY.330.001603
ORF1ab/nsp12560V560VgtCgtT2424AY.9.20.000882
ORF1ab/nsp12560V560VgtCgtT1722AY.1030.000106
ORF1ab/nsp12560V560VgtCgtA522AY.1030.000031
ORF1ab/nsp12560V560VgtCgtT2122AY.200.000816
ORF1ab/nsp12560V560VgtCgtA122AY.200.000039
ORF1ab/nsp12560V560VgtCgtT1920AY.250.000114
ORF1ab/nsp12560V560VgtCgtA120AY.250.000006
ORF1ab/nsp12560V560VgtCgtT1818B.1.177.800.034417
ORF1ab/nsp12560V560VgtCgtT1616B.1.1600.000499
ORF1ab/nsp12560V560VgtCgtT1616B.1.4000.006864
ORF1ab/nsp12560V560AgTcgCc1414All0.000003
ORF1ab/nsp12560V560VgtCgtT914B.10.000082
ORF1ab/nsp12560V560VgtCgtA514B.10.000046
ORF1ab/nsp12560V560FGtcTtc912All0.000002
ORF1ab/nsp12560V560FGtCTtT312All0.000001
ORF1ab/nsp12560V560VgtCgtT910AY.440.000055
ORF1ab/nsp12560V560VgtCgtA110AY.440.000006
ORF1ab/nsp12560V560VgtCgtT99AY.30.00009
ORF1ab/nsp12560V560VgtCgtT99AY.46.40.001481
ORF1ab/nsp12560V560VgtCgtT59P.10.000079
ORF1ab/nsp12560V560VgtCgtA49P.10.000063
ORF1ab/nsp12560V560VgtCgtT99Q.10.001137
ORF1ab/nsp12560V560VgtCgtT88B.1.4290.000188
ORF1ab/nsp12560V560GgTcgGc57All0.000001
ORF1ab/nsp12560V560GgTCgGG17All0
ORF1ab/nsp12560V560GgTCgGT17All0
ORF1ab/nsp12560V560VgtCgtT77AY.780.010786
ORF1ab/nsp12560V560VgtCgtA77B.1.4280.007143
ORF1ab/nsp12560V560VgtCgtT560.277778
ORF1ab/nsp12560V560FGtCTtT360.166667
ORF1ab/nsp12560V560FGtcTtc360.166667
ORF1ab/nsp12560V560VgtCgtG160.055556
ORF1ab/nsp12560V560VgtCgtT66B.1.1.5190.000238
ORF1ab/nsp12560V560VgtCgtT66B.1.1770.000079
ORF1ab/nsp12560V560GgTcgGc350.166667
ORF1ab/nsp12560V560GgTCgGT150.055556
ORF1ab/nsp12560V560GgTCgGG150.055556
ORF1ab/nsp12560V560IGtcAtc45All0.000001
ORF1ab/nsp12560V560IGtCAtT15All0
ORF1ab/nsp12560V560VgtCgtT55AY.3.10.000426
ORF1ab/nsp12560V560VgtCgtT55AY.470.000156
ORF1ab/nsp12560V560VgtCgtT55AY.98.10.000242
ORF1ab/nsp12560V560VgtCgtT55B.1.10.000091
ORF1ab/nsp12560V560VgtCgtG55B.1.5250.000566
ORF1ab/nsp12560V560del2GTc--c44All0.000001
ORF1ab/nsp12560V560DgTcgAc44All0.000001
ORF1ab/nsp12560V560del1Gtc-tc34All0.000001
ORF1ab/nsp12560V560LGtcCtc34All0.000001
ORF1ab/nsp12560V560del1gtCgt-14All0
ORF1ab/nsp12560V560LGtCTtA14All0
ORF1ab/nsp12560V560VgtCgtT44AY.260.000113
ORF1ab/nsp12560V560VgtCgtT44AY.50.000083
ORF1ab/nsp12560V560VgtCgtA34AY.610.000314
ORF1ab/nsp12560V560VgtCgtT14AY.610.000105
ORF1ab/nsp12560V560del2GTc--c44B.1.1.70.000004
ORF1ab/nsp12560V560delGTC---44B.1.1.70.000004
ORF1ab/nsp12560V560VgtCgtT24B.1.3510.000059
ORF1ab/nsp12560V560VgtCgtA24B.1.3510.000059
ORF1ab/nsp12560V560VgtCgtT33AY.1160.00086
ORF1ab/nsp12560V560VgtCgtT33AY.1210.000406
ORF1ab/nsp12560V560VgtCgtA23AY.390.000049
ORF1ab/nsp12560V560VgtCgtT13AY.390.000025
ORF1ab/nsp12560V560VgtCgtT33AY.4.20.000065
ORF1ab/nsp12560V560delGTC---33AY.430.000013
ORF1ab/nsp12560V560AgTcgCc33B.10.000027
ORF1ab/nsp12560V560VgtCgtT33B.1.1.2140.000166
ORF1ab/nsp12560V560AgTcgCc33B.1.1.70.000003
ORF1ab/nsp12560V560VgtCgtT33B.1.2430.000209
ORF1ab/nsp12560V560VgtCgtT33B.1.360.000438
ORF1ab/nsp12560V560VgtCgtT33B.1.36.170.001482
ORF1ab/nsp12560V560DgTcgAc220.111111
ORF1ab/nsp12560V560CGTCTGT120.055556
ORF1ab/nsp12560V560CGTcTGc120.055556
ORF1ab/nsp12560V560IGtcAtc12A.2.40.003367
ORF1ab/nsp12560V560IGtCAtT12A.2.40.003367
ORF1ab/nsp12560V560MGtCAtG22All0
ORF1ab/nsp12560V560EgTCgAA12All0
ORF1ab/nsp12560V560EgTCgAG12All0
ORF1ab/nsp12560V560CGTCTGT12All0
ORF1ab/nsp12560V560CGTcTGc12All0
ORF1ab/nsp12560V560SGTcTCc12All0
ORF1ab/nsp12560V560SGTcAGc12All0
ORF1ab/nsp12560V560delGTC---22AY.250.000012
ORF1ab/nsp12560V560VgtCgtA22AY.290.000032
ORF1ab/nsp12560V560AgTcgCc22AY.30.00002
ORF1ab/nsp12560V560VgtCgtT22AY.380.000999
ORF1ab/nsp12560V560delGTC---22AY.40.000003
ORF1ab/nsp12560V560VgtCgtT22AY.460.000208
ORF1ab/nsp12560V560VgtCgtA22AY.99.20.000184
ORF1ab/nsp12560V560FGtcTtc22B.10.000018
ORF1ab/nsp12560V560FGtcTtc22B.1.20.000018
ORF1ab/nsp12560V560VgtCgtT22B.1.5260.000047
ORF1ab/nsp12560V560VgtCgtT22B.1.5610.000794
ORF1ab/nsp12560V560VgtCgtA12D.20.000075
ORF1ab/nsp12560V560VgtCgtT12D.20.000075
ORF1ab/nsp12560V560delGTC---22P.10.000032
ORF1ab/nsp12560V560SGTcAGc110.055556
ORF1ab/nsp12560V560RGTCAGG110.055556
ORF1ab/nsp12560V560KGTCAAG110.055556
ORF1ab/nsp12560V560MGtCAtG110.055556
ORF1ab/nsp12560V560EgTCgAG110.055556
ORF1ab/nsp12560V560IGtcAtc110.055556
ORF1ab/nsp12560V560NGTcAAc110.055556
ORF1ab/nsp12560V560VgtCgtT11A.2.40.003367
ORF1ab/nsp12560V560FGtcTtc11A.2.40.003367
ORF1ab/nsp12560V560VgtCgtT11A.2.5.20.001572
ORF1ab/nsp12560V560VgtCgtT11A.50.001923
ORF1ab/nsp12560V560NGTcAAc11All0
ORF1ab/nsp12560V560KGTCAAG11All0
ORF1ab/nsp12560V560RGTCAGG11All0
ORF1ab/nsp12560V560VgtCgtT11AY.1000.000046
ORF1ab/nsp12560V560VgtCgtA11AY.1110.000183
ORF1ab/nsp12560V560VgtCgtT11AY.1180.000063
ORF1ab/nsp12560V560VgtCgtT11AY.1190.000035
ORF1ab/nsp12560V560VgtCgtT11AY.1200.000037
ORF1ab/nsp12560V560VgtCgtT11AY.20.000356
ORF1ab/nsp12560V560SGTcTCc11AY.250.000006
ORF1ab/nsp12560V560del1Gtc-tc11AY.250.000006
ORF1ab/nsp12560V560del1Gtc-tc11AY.30.00001
ORF1ab/nsp12560V560VgtCgtT11AY.340.000097
ORF1ab/nsp12560V560AgTcgCc11AY.390.000025
ORF1ab/nsp12560V560VgtCgtT11AY.4.50.000107
ORF1ab/nsp12560V560delGTC---11AY.420.00004
ORF1ab/nsp12560V560IGtcAtc11AY.430.000004
ORF1ab/nsp12560V560AgTcgCc11AY.440.000006
ORF1ab/nsp12560V560delGTC---11AY.440.000006
ORF1ab/nsp12560V560VgtCgtA11AY.5.40.000277
ORF1ab/nsp12560V560VgtCgtT11AY.560.001605
ORF1ab/nsp12560V560delGTC---11AY.590.00053
ORF1ab/nsp12560V560VgtCgtT11AY.60.000041
ORF1ab/nsp12560V560VgtCgtA11AY.660.00107
ORF1ab/nsp12560V560MGtCAtG11AY.670.000464
ORF1ab/nsp12560V560VgtCgtT11AY.740.000116
ORF1ab/nsp12560V560VgtCgtT11AY.750.000056
ORF1ab/nsp12560V560VgtCgtT11AY.790.001211
ORF1ab/nsp12560V560delGTC---11AY.840.000437
ORF1ab/nsp12560V560VgtCgtA11AY.920.000287
ORF1ab/nsp12560V560LGtcCtc11B.10.000009
ORF1ab/nsp12560V560GgTcgGc11B.10.000009
ORF1ab/nsp12560V560LGtCTtA11B.1.10.000018
ORF1ab/nsp12560V560delGTC---11B.1.10.000018
ORF1ab/nsp12560V560VgtCgtT11B.1.1.1010.01
ORF1ab/nsp12560V560delGTC---11B.1.1.1390.022727
ORF1ab/nsp12560V560VgtCgtT11B.1.1.2650.003155
ORF1ab/nsp12560V560VgtCgtT11B.1.1.3040.002809
ORF1ab/nsp12560V560del1Gtc-tc11B.1.1.70.000001
ORF1ab/nsp12560V560DgTcgAc11B.1.1.70.000001
ORF1ab/nsp12560V560VgtCgtT11B.1.1490.003425
ORF1ab/nsp12560V560delGTC---11B.1.160.230.004831
ORF1ab/nsp12560V560delGTC---11B.1.177.540.000606
ORF1ab/nsp12560V560delGTC---11B.1.177.680.015152
ORF1ab/nsp12560V560AgTcgCc11B.1.177.730.000566
ORF1ab/nsp12560V560LGtcCtc11B.1.20.000009
ORF1ab/nsp12560V560AgTcgCc11B.1.20.000009
ORF1ab/nsp12560V560VgtCgtT11B.1.2410.000812
ORF1ab/nsp12560V560VgtCgtA11B.1.2580.000067
ORF1ab/nsp12560V560VgtCgtA11B.1.258.170.000104
ORF1ab/nsp12560V560VgtCgtT11B.1.258.50.008772
ORF1ab/nsp12560V560VgtCgtT11B.1.2980.002114
ORF1ab/nsp12560V560VgtCgtT11B.1.3690.000285
ORF1ab/nsp12560V560EgTCgAA11B.1.4160.001269
ORF1ab/nsp12560V560AgTcgCc11B.1.4270.00005
ORF1ab/nsp12560V560VgtCgtT11B.1.4360.001029
ORF1ab/nsp12560V560VgtCgtT11B.1.438.10.000107
ORF1ab/nsp12560V560VgtCgtT11B.1.466.20.000391
ORF1ab/nsp12560V560VgtCgtT11B.1.5580.004566
ORF1ab/nsp12560V560VgtCgtT11B.1.5760.000907
ORF1ab/nsp12560V560IGtcAtc11B.1.5960.000087
ORF1ab/nsp12560V560GgTcgGc11B.1.617.20.000004
ORF1ab/nsp12560V560del1gtCgt-11B.1.617.20.000004
ORF1ab/nsp12560V560FGtcTtc11B.1.617.20.000004
ORF1ab/nsp12560V560VgtCgtT11B.30.000831
ORF1ab/nsp12560V560DgTcgAc11B.40.002208
ORF1ab/nsp12560V560VgtCgtT11B.60.00091
ORF1ab/nsp12560V560VgtCgtT11B.600.015873
ORF1ab/nsp12560V560AgTcgCc11C.350.000774
ORF1ab/nsp12560V560LGtcCtc11P.10.000016
ORF1ab/nsp12560V560delGTC---11P.1.40.000977
ORF1ab/nsp12560V560delGTC---11Q.20.000613
ORF1ab/nsp12560V560VgtCgtT11Q.80.000165
ORF1ab/nsp12560V560VgtCgtT11W.40.001351

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.