CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 562

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/nsp12562I562VI4954VnonsynAtcGtc6946920.99711815124-15126
ORF1ab/nsp12562I562VI4954VnonsynAtCGtT69420.0028818415124-15126
ORF1ab/nsp12562I562II4954IsynatCatT5084220.83070915124-15126
ORF1ab/nsp12562I562II4954IsynatCatA508860.16929115124-15126
ORF1ab/nsp12562I562LI4954LnonsynAtcCtc41320.78048815124-15126
ORF1ab/nsp12562I562LI4954LnonsynAtCTtA4160.14634115124-15126
ORF1ab/nsp12562I562LI4954LnonsynAtCTtG4120.048780515124-15126
ORF1ab/nsp12562I562LI4954LnonsynAtCCtT4110.024390215124-15126
ORF1ab/nsp12562I562delI4954deldelATC---1616115124-15126
ORF1ab/nsp12562I562TI4954TnonsynaTcaCc1212115124-15126
ORF1ab/nsp12562I562FI4954FnonsynAtcTtc55115124-15126
ORF1ab/nsp12562I562NI4954NnonsynaTcaAc44115124-15126
ORF1ab/nsp12562I562XI4954XnonsynATCTAG420.515124-15126
ORF1ab/nsp12562I562XI4954XnonsynATCTGA410.2515124-15126
ORF1ab/nsp12562I562XI4954XnonsynATCTAA410.2515124-15126
ORF1ab/nsp12562I562MI4954MnonsynatCatG33115124-15126
ORF1ab/nsp12562I562SI4954SnonsynaTcaGc33115124-15126
ORF1ab/nsp12562I562KI4954KnonsynaTCaAG320.66666715124-15126
ORF1ab/nsp12562I562KI4954KnonsynaTCaAA310.33333315124-15126
ORF1ab/nsp12562I562QI4954QnonsynATCCAG22115124-15126
ORF1ab/nsp12562I562YI4954YnonsynATcTAc22115124-15126
ORF1ab/nsp12562I562RI4954RnonsynaTCaGG210.515124-15126
ORF1ab/nsp12562I562RI4954RnonsynaTCaGA210.515124-15126
ORF1ab/nsp12562I562del1I4954del1delAtc-tc11115124-15126
ORF1ab/nsp12562I562WI4954WnonsynATCTGG11115124-15126
ORF1ab/nsp12562I562CI4954CnonsynATcTGc11115124-15126
ORF1ab/nsp12562I562PI4954PnonsynATcCCc11115124-15126

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/nsp12562I562VAtcGtc692694All0.000132
ORF1ab/nsp12562I562VAtCGtT2694All0
ORF1ab/nsp12562I562IatCatT422508All0.000081
ORF1ab/nsp12562I562IatCatA86508All0.000016
ORF1ab/nsp12562I562VAtcGtc326326B.1.617.20.001228
ORF1ab/nsp12562I562IatCatT7790B.1.1.70.000069
ORF1ab/nsp12562I562IatCatA1390B.1.1.70.000012
ORF1ab/nsp12562I562VAtcGtc8686AY.440.000523
ORF1ab/nsp12562I562VAtcGtc4444AY.430.000195
ORF1ab/nsp12562I562LAtcCtc3241All0.000006
ORF1ab/nsp12562I562LAtCTtA641All0.000001
ORF1ab/nsp12562I562LAtCTtG241All0
ORF1ab/nsp12562I562LAtCCtT141All0
ORF1ab/nsp12562I562IatCatA3641P.1.140.001721
ORF1ab/nsp12562I562IatCatT541P.1.140.000239
ORF1ab/nsp12562I562VAtcGtc3838AY.40.000059
ORF1ab/nsp12562I562IatCatT3737B.1.1770.000487
ORF1ab/nsp12562I562IatCatT2727AY.250.000162
ORF1ab/nsp12562I562IatCatT2727B.1.20.000238
ORF1ab/nsp12562I562IatCatT2125AY.40.000033
ORF1ab/nsp12562I562IatCatA425AY.40.000006
ORF1ab/nsp12562I562IatCatT2021B.1.617.20.000075
ORF1ab/nsp12562I562IatCatA121B.1.617.20.000004
ORF1ab/nsp12562I562IatCatT1919A.180.95
ORF1ab/nsp12562I562VAtcGtc1919AY.250.000114
ORF1ab/nsp12562I562IatCatT1618B.10.000147
ORF1ab/nsp12562I562IatCatA218B.10.000018
ORF1ab/nsp12562I562IatCatT1818B.1.1600.000561
ORF1ab/nsp12562I562delATC---1616All0.000003
ORF1ab/nsp12562I562VAtcGtc1515AY.390.000371
ORF1ab/nsp12562I562VAtcGtc1515B.1.10.000272
ORF1ab/nsp12562I562VAtcGtc1313AY.30.000129
ORF1ab/nsp12562I562IatCatT913AY.430.00004
ORF1ab/nsp12562I562IatCatA413AY.430.000018
ORF1ab/nsp12562I562TaTcaCc1212All0.000002
ORF1ab/nsp12562I562VAtcGtc1212AY.1190.000424
ORF1ab/nsp12562I562LAtcCtc1212B.1.2320.006448
ORF1ab/nsp12562I562LAtcCtc1011B.1.1.70.000009
ORF1ab/nsp12562I562LAtCCtT111B.1.1.70.000001
ORF1ab/nsp12562I562VAtcGtc1111P.10.000173
ORF1ab/nsp12562I562VAtcGtc1010AY.450.001217
ORF1ab/nsp12562I562IatCatA710B.1.5250.000792
ORF1ab/nsp12562I562IatCatT310B.1.5250.000339
ORF1ab/nsp12562I562IatCatT89AY.30.00008
ORF1ab/nsp12562I562IatCatA19AY.30.00001
ORF1ab/nsp12562I562IatCatT69AY.440.000037
ORF1ab/nsp12562I562IatCatA39AY.440.000018
ORF1ab/nsp12562I562IatCatT99B.1.1.3160.008326
ORF1ab/nsp12562I562LAtCTtA580.277778
ORF1ab/nsp12562I562LAtCTtG280.111111
ORF1ab/nsp12562I562LAtcCtc180.055556
ORF1ab/nsp12562I562IatCatT88B.1.177.810.001515
ORF1ab/nsp12562I562IatCatT77B.1.10.000127
ORF1ab/nsp12562I562VAtcGtc77B.1.1.70.000006
ORF1ab/nsp12562I562VAtcGtc66AY.1030.000037
ORF1ab/nsp12562I562VAtcGtc66AY.470.000187
ORF1ab/nsp12562I562IatCatT66AY.730.003992
ORF1ab/nsp12562I562VAtcGtc66B.1.20.000053
ORF1ab/nsp12562I562VAtcGtc66B.1.3510.000178
ORF1ab/nsp12562I562IatCatT66P.10.000095
ORF1ab/nsp12562I562FAtcTtc55All0.000001
ORF1ab/nsp12562I562IatCatT45AY.1030.000025
ORF1ab/nsp12562I562IatCatA15AY.1030.000006
ORF1ab/nsp12562I562IatCatT55AY.4.20.000108
ORF1ab/nsp12562I562IatCatT55AY.50.000103
ORF1ab/nsp12562I562VAtcGtc55B.10.000046
ORF1ab/nsp12562I562IatCatT55C.370.00058
ORF1ab/nsp12562I562XATCTAG240.111111
ORF1ab/nsp12562I562XATCTAA140.055556
ORF1ab/nsp12562I562XATCTGA140.055556
ORF1ab/nsp12562I562NaTcaAc44All0.000001
ORF1ab/nsp12562I562XATCTAG24All0
ORF1ab/nsp12562I562XATCTGA14All0
ORF1ab/nsp12562I562XATCTAA14All0
ORF1ab/nsp12562I562VAtcGtc44AY.1100.000451
ORF1ab/nsp12562I562VAtcGtc44AY.200.000155
ORF1ab/nsp12562I562VAtcGtc44AY.4.50.00043
ORF1ab/nsp12562I562IatCatT44B.1.36.170.001976
ORF1ab/nsp12562I562VAtcGtc44B.1.5750.001214
ORF1ab/nsp12562I562KaTCaAG230.111111
ORF1ab/nsp12562I562KaTCaAA130.055556
ORF1ab/nsp12562I562VAtcGtc33A.2.5.30.030928
ORF1ab/nsp12562I562IatCatT33A.210.00831
ORF1ab/nsp12562I562SaTcaGc33All0.000001
ORF1ab/nsp12562I562MatCatG33All0.000001
ORF1ab/nsp12562I562KaTCaAG23All0
ORF1ab/nsp12562I562KaTCaAA13All0
ORF1ab/nsp12562I562IatCatT33AY.1200.000112
ORF1ab/nsp12562I562IatCatT33AY.290.000047
ORF1ab/nsp12562I562VAtcGtc33AY.34.10.00153
ORF1ab/nsp12562I562VAtcGtc33AY.50.000062
ORF1ab/nsp12562I562IatCatA23AY.60.000082
ORF1ab/nsp12562I562IatCatT13AY.60.000041
ORF1ab/nsp12562I562VAtcGtc33AY.980.000237
ORF1ab/nsp12562I562IatCatT33B.1.1.2530.007519
ORF1ab/nsp12562I562IatCatT33B.1.2320.001612
ORF1ab/nsp12562I562IatCatA23B.1.4290.000047
ORF1ab/nsp12562I562IatCatT13B.1.4290.000024
ORF1ab/nsp12562I562MatCatG220.111111
ORF1ab/nsp12562I562NaTcaAc220.111111
ORF1ab/nsp12562I562YATcTAc220.111111
ORF1ab/nsp12562I562QATCCAG220.111111
ORF1ab/nsp12562I562VAtCGtT220.111111
ORF1ab/nsp12562I562FAtcTtc220.111111
ORF1ab/nsp12562I562RaTCaGA120.055556
ORF1ab/nsp12562I562RaTCaGG120.055556
ORF1ab/nsp12562I562IatCatA12A.10.000282
ORF1ab/nsp12562I562IatCatT12A.10.000282
ORF1ab/nsp12562I562IatCatT22A.190.018868
ORF1ab/nsp12562I562QATCCAG22All0
ORF1ab/nsp12562I562YATcTAc22All0
ORF1ab/nsp12562I562RaTCaGG12All0
ORF1ab/nsp12562I562RaTCaGA12All0
ORF1ab/nsp12562I562VAtcGtc22AY.1020.000053
ORF1ab/nsp12562I562IatCatA12AY.200.000039
ORF1ab/nsp12562I562IatCatT12AY.200.000039
ORF1ab/nsp12562I562VAtcGtc22AY.240.000862
ORF1ab/nsp12562I562VAtcGtc22AY.330.000134
ORF1ab/nsp12562I562VAtcGtc22AY.350.000466
ORF1ab/nsp12562I562VAtcGtc22AY.39.10.000079
ORF1ab/nsp12562I562delATC---22AY.40.000003
ORF1ab/nsp12562I562delATC---22AY.430.000009
ORF1ab/nsp12562I562LAtcCtc22AY.450.000243
ORF1ab/nsp12562I562VAtcGtc22AY.460.000208
ORF1ab/nsp12562I562VAtcGtc22AY.550.001835
ORF1ab/nsp12562I562VAtcGtc22AY.860.00166
ORF1ab/nsp12562I562IatCatT22AY.9.2.10.003953
ORF1ab/nsp12562I562IatCatT22AY.98.10.000097
ORF1ab/nsp12562I562TaTcaCc22B.10.000018
ORF1ab/nsp12562I562IatCatT22B.1.1.5190.000079
ORF1ab/nsp12562I562IatCatT22B.1.1.700.000682
ORF1ab/nsp12562I562VAtcGtc22B.1.1770.000026
ORF1ab/nsp12562I562IatCatT22B.1.177.40.000422
ORF1ab/nsp12562I562VAtcGtc22B.1.2060.001631
ORF1ab/nsp12562I562IatCatT22B.1.2210.000142
ORF1ab/nsp12562I562IatCatT22B.1.2580.000133
ORF1ab/nsp12562I562IatCatT22B.1.36.70.008
ORF1ab/nsp12562I562IatCatT12B.1.6120.002653
ORF1ab/nsp12562I562IatCatA12B.1.6120.002653
ORF1ab/nsp12562I562TaTcaCc22D.20.00015
ORF1ab/nsp12562I562delATC---22P.10.000032
ORF1ab/nsp12562I562VAtcGtc22P.1.80.009569
ORF1ab/nsp12562I562IatCatT22R.10.00018
ORF1ab/nsp12562I562CATcTGc110.055556
ORF1ab/nsp12562I562WATCTGG110.055556
ORF1ab/nsp12562I562SaTcaGc110.055556
ORF1ab/nsp12562I562IatCatA110.055556
ORF1ab/nsp12562I562SaTcaGc11A0.000387
ORF1ab/nsp12562I562IatCatT11A0.000387
ORF1ab/nsp12562I562IatCatT11A.2.50.000499
ORF1ab/nsp12562I562PATcCCc11All0
ORF1ab/nsp12562I562del1Atc-tc11All0
ORF1ab/nsp12562I562WATCTGG11All0
ORF1ab/nsp12562I562CATcTGc11All0
ORF1ab/nsp12562I562IatCatT11AY.1020.000027
ORF1ab/nsp12562I562VAtcGtc11AY.1050.000643
ORF1ab/nsp12562I562VAtcGtc11AY.110.001339
ORF1ab/nsp12562I562IatCatT11AY.1100.000113
ORF1ab/nsp12562I562IatCatT11AY.1110.000183
ORF1ab/nsp12562I562TaTcaCc11AY.1130.000142
ORF1ab/nsp12562I562VAtcGtc11AY.1160.000287
ORF1ab/nsp12562I562IatCatT11AY.1190.000035
ORF1ab/nsp12562I562VAtcGtc11AY.16.10.00047
ORF1ab/nsp12562I562delATC---11AY.250.000006
ORF1ab/nsp12562I562VAtcGtc11AY.260.000028
ORF1ab/nsp12562I562FAtcTtc11AY.30.00001
ORF1ab/nsp12562I562IatCatT11AY.340.000097
ORF1ab/nsp12562I562IatCatT11AY.360.000148
ORF1ab/nsp12562I562VAtcGtc11AY.370.000316
ORF1ab/nsp12562I562TaTcaCc11AY.39.10.00004
ORF1ab/nsp12562I562VAtcGtc11AY.4.2.10.000149
ORF1ab/nsp12562I562IatCatA11AY.400.000964
ORF1ab/nsp12562I562IatCatT11AY.420.00004
ORF1ab/nsp12562I562delATC---11AY.420.00004
ORF1ab/nsp12562I562LAtcCtc11AY.430.000004
ORF1ab/nsp12562I562PATcCCc11AY.430.000004
ORF1ab/nsp12562I562TaTcaCc11AY.440.000006
ORF1ab/nsp12562I562delATC---11AY.440.000006
ORF1ab/nsp12562I562LAtcCtc11AY.440.000006
ORF1ab/nsp12562I562IatCatT11AY.46.50.000198
ORF1ab/nsp12562I562IatCatT11AY.470.000031
ORF1ab/nsp12562I562delATC---11AY.590.00053
ORF1ab/nsp12562I562IatCatT11AY.610.000105
ORF1ab/nsp12562I562IatCatA11AY.670.000464
ORF1ab/nsp12562I562VAtcGtc11AY.7.10.000113
ORF1ab/nsp12562I562IatCatA11AY.7.10.000113
ORF1ab/nsp12562I562LAtcCtc11AY.750.000056
ORF1ab/nsp12562I562VAtcGtc11AY.820.001357
ORF1ab/nsp12562I562VAtcGtc11AY.840.000437
ORF1ab/nsp12562I562VAtcGtc11AY.850.000427
ORF1ab/nsp12562I562VAtcGtc11AY.870.000833
ORF1ab/nsp12562I562VAtcGtc11AY.9.20.000037
ORF1ab/nsp12562I562IatCatT11AY.980.000079
ORF1ab/nsp12562I562VAtcGtc11AY.98.10.000048
ORF1ab/nsp12562I562MatCatG11AY.990.001049
ORF1ab/nsp12562I562SaTcaGc11B0.000128
ORF1ab/nsp12562I562LAtCTtA11B.10.000009
ORF1ab/nsp12562I562NaTcaAc11B.10.000009
ORF1ab/nsp12562I562FAtcTtc11B.10.000009
ORF1ab/nsp12562I562LAtcCtc11B.1.10.000018
ORF1ab/nsp12562I562del1Atc-tc11B.1.10.000018
ORF1ab/nsp12562I562LAtcCtc11B.1.1.10.000327
ORF1ab/nsp12562I562delATC---11B.1.1.1390.022727
ORF1ab/nsp12562I562LAtcCtc11B.1.1.2160.00089
ORF1ab/nsp12562I562IatCatT11B.1.1.2220.000204
ORF1ab/nsp12562I562IatCatT11B.1.1.3060.000438
ORF1ab/nsp12562I562VAtcGtc11B.1.1.3160.000925
ORF1ab/nsp12562I562IatCatT11B.1.1.370.000193
ORF1ab/nsp12562I562delATC---11B.1.1.70.000001
ORF1ab/nsp12562I562IatCatT11B.1.1260.001276
ORF1ab/nsp12562I562TaTcaCc11B.1.130.002375
ORF1ab/nsp12562I562TaTcaCc11B.1.1600.000031
ORF1ab/nsp12562I562delATC---11B.1.160.230.004831
ORF1ab/nsp12562I562IatCatT11B.1.177.330.001645
ORF1ab/nsp12562I562delATC---11B.1.177.540.000606
ORF1ab/nsp12562I562delATC---11B.1.177.680.015152
ORF1ab/nsp12562I562IatCatA11B.1.177.730.000566
ORF1ab/nsp12562I562VAtcGtc11B.1.2180.005155
ORF1ab/nsp12562I562TaTcaCc11B.1.2210.000071
ORF1ab/nsp12562I562IatCatT11B.1.2340.000132
ORF1ab/nsp12562I562IatCatT11B.1.2400.000216
ORF1ab/nsp12562I562IatCatT11B.1.3510.00003
ORF1ab/nsp12562I562FAtcTtc11B.1.36.350.002604
ORF1ab/nsp12562I562LAtcCtc11B.1.3620.001541
ORF1ab/nsp12562I562IatCatT11B.1.3900.010638
ORF1ab/nsp12562I562NaTcaAc11B.1.3980.002976
ORF1ab/nsp12562I562IatCatT11B.1.438.10.000107
ORF1ab/nsp12562I562IatCatT11B.1.4990.00105
ORF1ab/nsp12562I562IatCatT11B.1.5600.00463
ORF1ab/nsp12562I562IatCatT11B.1.5750.000303
ORF1ab/nsp12562I562TaTcaCc11B.1.5800.004065
ORF1ab/nsp12562I562IatCatA11B.1.5960.000087
ORF1ab/nsp12562I562TaTcaCc11B.1.617.20.000004
ORF1ab/nsp12562I562IatCatT11B.1.619.10.000641
ORF1ab/nsp12562I562IatCatA11B.1.6360.006711
ORF1ab/nsp12562I562IatCatT11B.470.020408
ORF1ab/nsp12562I562IatCatT11C.10.002392
ORF1ab/nsp12562I562VAtcGtc11C.10.002392
ORF1ab/nsp12562I562delATC---11P.1.40.000977
ORF1ab/nsp12562I562IatCatT11P.60.003145

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.