CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp3 : CodonNum = 1546

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/nsp31546L1546FL2364FnonsynCttTtt32532517355-7357
ORF1ab/nsp31546L1546LL2364LsynctTctC2332000.8583697355-7357
ORF1ab/nsp31546L1546LL2364LsynctTctG233280.1201727355-7357
ORF1ab/nsp31546L1546LL2364LsynctTctA23350.02145927355-7357
ORF1ab/nsp31546L1546IL2364InonsynCttAtt81800.9876547355-7357
ORF1ab/nsp31546L1546IL2364InonsynCtTAtA8110.01234577355-7357
ORF1ab/nsp31546L1546delL2364deldelCTT---686817355-7357
ORF1ab/nsp31546L1546PL2364PnonsyncTtcCt1090.97355-7357
ORF1ab/nsp31546L1546PL2364PnonsyncTTcCG1010.17355-7357
ORF1ab/nsp31546L1546RL2364RnonsyncTtcGt4417355-7357
ORF1ab/nsp31546L1546HL2364HnonsyncTtcAt3317355-7357
ORF1ab/nsp31546L1546del1L2364del1delctTct-320.6666677355-7357
ORF1ab/nsp31546L1546del1L2364del1delcTtc-t310.3333337355-7357
ORF1ab/nsp31546L1546SL2364SnonsynCTtTCt210.57355-7357
ORF1ab/nsp31546L1546SL2364SnonsynCTTAGC210.57355-7357
ORF1ab/nsp31546L1546XL2364XnonsynCTTTAA1117355-7357
ORF1ab/nsp31546L1546YL2364YnonsynCTtTAt1117355-7357
ORF1ab/nsp31546L1546VL2364VnonsynCttGtt1117355-7357

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/nsp31546L1546FCttTtt325325All0.000062
ORF1ab/nsp31546L1546LctTctC200233All0.000038
ORF1ab/nsp31546L1546LctTctG28233All0.000005
ORF1ab/nsp31546L1546LctTctA5233All0.000001
ORF1ab/nsp31546L1546ICttAtt8081All0.000015
ORF1ab/nsp31546L1546ICtTAtA181All0
ORF1ab/nsp31546L1546delCTT---6868All0.000013
ORF1ab/nsp31546L1546LctTctC5656B.1.1.1231
ORF1ab/nsp31546L1546ICttAtt5555AY.50.001136
ORF1ab/nsp31546L1546FCttTtt4040AY.1030.000248
ORF1ab/nsp31546L1546FCttTtt4040AY.40.000062
ORF1ab/nsp31546L1546FCttTtt3434B.1.617.20.000128
ORF1ab/nsp31546L1546LctTctC2727AY.440.000164
ORF1ab/nsp31546L1546LctTctG2626B.1.5610.010322
ORF1ab/nsp31546L1546FCttTtt1818AY.560.028892
ORF1ab/nsp31546L1546FCttTtt1717AY.1190.0006
ORF1ab/nsp31546L1546delCTT---1717B.1.1.70.000015
ORF1ab/nsp31546L1546FCttTtt1414AY.250.000084
ORF1ab/nsp31546L1546FCttTtt1414AY.430.000062
ORF1ab/nsp31546L1546FCttTtt1212AY.1020.000318
ORF1ab/nsp31546L1546LctTctC1212B.1.617.20.000045
ORF1ab/nsp31546L1546FCttTtt1111AY.390.000272
ORF1ab/nsp31546L1546LctTctC1111B.1.1.70.00001
ORF1ab/nsp31546L1546PcTtcCt910All0.000002
ORF1ab/nsp31546L1546PcTTcCG110All0
ORF1ab/nsp31546L1546LctTctC1010B.1.1.630.003858
ORF1ab/nsp31546L1546FCttTtt1010B.1.1.70.000009
ORF1ab/nsp31546L1546FCttTtt1010B.1.20.000088
ORF1ab/nsp31546L1546LctTctC88AY.30.00008
ORF1ab/nsp31546L1546LctTctC88AY.430.000035
ORF1ab/nsp31546L1546FCttTtt88AY.440.000049
ORF1ab/nsp31546L1546LctTctC77AY.1020.000186
ORF1ab/nsp31546L1546FCttTtt77AY.200.000272
ORF1ab/nsp31546L1546LctTctC77AY.40.000011
ORF1ab/nsp31546L1546delCTT---77AY.430.000031
ORF1ab/nsp31546L1546LctTctC77B.1.20.000062
ORF1ab/nsp31546L1546FCttTtt66AY.30.00006
ORF1ab/nsp31546L1546delCTT---66B.1.617.20.000023
ORF1ab/nsp31546L1546LctTctC66P.10.000095
ORF1ab/nsp31546L1546RcTtcGt44All0.000001
ORF1ab/nsp31546L1546FCttTtt44AY.1130.00057
ORF1ab/nsp31546L1546FCttTtt44AY.340.000388
ORF1ab/nsp31546L1546FCttTtt44AY.50.000083
ORF1ab/nsp31546L1546FCttTtt44AY.540.000381
ORF1ab/nsp31546L1546delCTT---44B.10.000037
ORF1ab/nsp31546L1546LctTctC44B.1.1.2720.020833
ORF1ab/nsp31546L1546FCttTtt44B.1.1.5190.000159
ORF1ab/nsp31546L1546FCttTtt44C.160.004242
ORF1ab/nsp31546L1546HcTtcAt33All0.000001
ORF1ab/nsp31546L1546del1ctTct-23All0
ORF1ab/nsp31546L1546del1cTtc-t13All0
ORF1ab/nsp31546L1546FCttTtt33AY.1110.000549
ORF1ab/nsp31546L1546LctTctC33AY.240.001293
ORF1ab/nsp31546L1546FCttTtt33AY.260.000085
ORF1ab/nsp31546L1546LctTctC33AY.46.60.000217
ORF1ab/nsp31546L1546FCttTtt33AY.470.000093
ORF1ab/nsp31546L1546FCttTtt33B.10.000027
ORF1ab/nsp31546L1546FCttTtt33B.1.1.2840.000322
ORF1ab/nsp31546L1546ICttAtt33B.1.1.70.000003
ORF1ab/nsp31546L1546FCttTtt33B.1.2580.0002
ORF1ab/nsp31546L1546FCttTtt33P.1.150.000697
ORF1ab/nsp31546L1546LctTctA220.111111
ORF1ab/nsp31546L1546SCTtTCt12All0
ORF1ab/nsp31546L1546SCTTAGC12All0
ORF1ab/nsp31546L1546FCttTtt22AY.1060.00067
ORF1ab/nsp31546L1546LctTctA22AY.200.000078
ORF1ab/nsp31546L1546FCttTtt22AY.230.000139
ORF1ab/nsp31546L1546ICttAtt22AY.290.000032
ORF1ab/nsp31546L1546FCttTtt22AY.330.000134
ORF1ab/nsp31546L1546FCttTtt22AY.39.10.000079
ORF1ab/nsp31546L1546LctTctC22AY.420.00008
ORF1ab/nsp31546L1546delCTT---22AY.420.00008
ORF1ab/nsp31546L1546ICttAtt22AY.440.000012
ORF1ab/nsp31546L1546LctTctC22AY.450.000243
ORF1ab/nsp31546L1546ICttAtt22AY.46.50.000397
ORF1ab/nsp31546L1546ICttAtt22B.10.000018
ORF1ab/nsp31546L1546del1ctTct-22B.10.000018
ORF1ab/nsp31546L1546LctTctC22B.10.000018
ORF1ab/nsp31546L1546LctTctA12B.1.10.000018
ORF1ab/nsp31546L1546LctTctC12B.1.10.000018
ORF1ab/nsp31546L1546HcTtcAt22B.1.1.70.000002
ORF1ab/nsp31546L1546RcTtcGt22B.1.160.90.014388
ORF1ab/nsp31546L1546LctTctC22B.1.1770.000026
ORF1ab/nsp31546L1546LctTctC22B.1.177.210.000153
ORF1ab/nsp31546L1546delCTT---22B.1.20.000018
ORF1ab/nsp31546L1546FCttTtt22B.1.2430.000139
ORF1ab/nsp31546L1546delCTT---22B.1.4970.00063
ORF1ab/nsp31546L1546LctTctC22B.1.617.10.000258
ORF1ab/nsp31546L1546FCttTtt22B.1.617.10.000258
ORF1ab/nsp31546L1546ICttAtt22B.1.617.20.000008
ORF1ab/nsp31546L1546FCttTtt110.055556
ORF1ab/nsp31546L1546FCttTtt11AD.20.000219
ORF1ab/nsp31546L1546ICttAtt11AF.10.037037
ORF1ab/nsp31546L1546YCTtTAt11All0
ORF1ab/nsp31546L1546VCttGtt11All0
ORF1ab/nsp31546L1546XCTTTAA11All0
ORF1ab/nsp31546L1546FCttTtt11AY.1000.000046
ORF1ab/nsp31546L1546ICttAtt11AY.1020.000027
ORF1ab/nsp31546L1546HcTtcAt11AY.1030.000006
ORF1ab/nsp31546L1546LctTctC11AY.1030.000006
ORF1ab/nsp31546L1546delCTT---11AY.1030.000006
ORF1ab/nsp31546L1546delCTT---11AY.1130.000142
ORF1ab/nsp31546L1546FCttTtt11AY.1180.000063
ORF1ab/nsp31546L1546FCttTtt11AY.1200.000037
ORF1ab/nsp31546L1546delCTT---11AY.120.20.001285
ORF1ab/nsp31546L1546FCttTtt11AY.1210.000135
ORF1ab/nsp31546L1546LctTctC11AY.160.00038
ORF1ab/nsp31546L1546FCttTtt11AY.23.10.000417
ORF1ab/nsp31546L1546FCttTtt11AY.240.000431
ORF1ab/nsp31546L1546ICttAtt11AY.250.000006
ORF1ab/nsp31546L1546delCTT---11AY.250.000006
ORF1ab/nsp31546L1546LctTctC11AY.290.000016
ORF1ab/nsp31546L1546ICttAtt11AY.30.00001
ORF1ab/nsp31546L1546delCTT---11AY.3.10.000085
ORF1ab/nsp31546L1546delCTT---11AY.330.000067
ORF1ab/nsp31546L1546LctTctC11AY.340.000097
ORF1ab/nsp31546L1546FCttTtt11AY.350.000233
ORF1ab/nsp31546L1546LctTctC11AY.360.000148
ORF1ab/nsp31546L1546LctTctC11AY.390.000025
ORF1ab/nsp31546L1546ICttAtt11AY.40.000002
ORF1ab/nsp31546L1546delCTT---11AY.40.000002
ORF1ab/nsp31546L1546FCttTtt11AY.4.20.000022
ORF1ab/nsp31546L1546delCTT---11AY.440.000006
ORF1ab/nsp31546L1546PcTtcCt11AY.440.000006
ORF1ab/nsp31546L1546FCttTtt11AY.450.000122
ORF1ab/nsp31546L1546PcTtcCt11AY.460.000104
ORF1ab/nsp31546L1546FCttTtt11AY.46.20.000635
ORF1ab/nsp31546L1546delCTT---11AY.46.60.000072
ORF1ab/nsp31546L1546LctTctC11AY.50.000021
ORF1ab/nsp31546L1546delCTT---11AY.50.000021
ORF1ab/nsp31546L1546FCttTtt11AY.5.30.000337
ORF1ab/nsp31546L1546delCTT---11AY.660.00107
ORF1ab/nsp31546L1546delCTT---11AY.750.000056
ORF1ab/nsp31546L1546ICttAtt11AY.880.000884
ORF1ab/nsp31546L1546delCTT---11AY.90.000068
ORF1ab/nsp31546L1546FCttTtt11AY.90.000068
ORF1ab/nsp31546L1546delCTT---11AY.9.20.000037
ORF1ab/nsp31546L1546LctTctG11AY.9.20.000037
ORF1ab/nsp31546L1546ICttAtt11AY.98.10.000048
ORF1ab/nsp31546L1546FCttTtt11AY.99.20.000092
ORF1ab/nsp31546L1546FCttTtt11B.1.10.000018
ORF1ab/nsp31546L1546delCTT---11B.1.10.000018
ORF1ab/nsp31546L1546ICttAtt11B.1.10.000018
ORF1ab/nsp31546L1546LctTctC11B.1.1.10.000327
ORF1ab/nsp31546L1546FCttTtt11B.1.1.10.000327
ORF1ab/nsp31546L1546FCttTtt11B.1.1.1530.001095
ORF1ab/nsp31546L1546delCTT---11B.1.1.2210.010101
ORF1ab/nsp31546L1546LctTctG11B.1.1.2220.000204
ORF1ab/nsp31546L1546delCTT---11B.1.1.3060.000438
ORF1ab/nsp31546L1546ICttAtt11B.1.1.3060.000438
ORF1ab/nsp31546L1546LctTctC11B.1.1.3160.000925
ORF1ab/nsp31546L1546FCttTtt11B.1.1.390.00051
ORF1ab/nsp31546L1546delCTT---11B.1.1.4480.002033
ORF1ab/nsp31546L1546delCTT---11B.1.1.460.004367
ORF1ab/nsp31546L1546delCTT---11B.1.1.5190.00004
ORF1ab/nsp31546L1546ICttAtt11B.1.1.5190.00004
ORF1ab/nsp31546L1546del1cTtc-t11B.1.1.70.000001
ORF1ab/nsp31546L1546SCTtTCt11B.1.1.70.000001
ORF1ab/nsp31546L1546XCTTTAA11B.1.1.70.000001
ORF1ab/nsp31546L1546PcTtcCt11B.1.1.70.000001
ORF1ab/nsp31546L1546FCttTtt11B.1.1460.004237
ORF1ab/nsp31546L1546FCttTtt11B.1.1600.000031
ORF1ab/nsp31546L1546LctTctC11B.1.1600.000031
ORF1ab/nsp31546L1546RcTtcGt11B.1.160.220.006757
ORF1ab/nsp31546L1546delCTT---11B.1.1610.017241
ORF1ab/nsp31546L1546FCttTtt11B.1.1770.000013
ORF1ab/nsp31546L1546FCttTtt11B.1.177.210.000076
ORF1ab/nsp31546L1546VCttGtt11B.1.20.000009
ORF1ab/nsp31546L1546PcTtcCt11B.1.20.000009
ORF1ab/nsp31546L1546RcTtcGt11B.1.2360.002053
ORF1ab/nsp31546L1546delCTT---11B.1.2580.000067
ORF1ab/nsp31546L1546delCTT---11B.1.3510.00003
ORF1ab/nsp31546L1546LctTctC11B.1.3510.00003
ORF1ab/nsp31546L1546ICtTAtA11B.1.3550.011111
ORF1ab/nsp31546L1546PcTtcCt11B.1.3550.011111
ORF1ab/nsp31546L1546LctTctC11B.1.36.80.001
ORF1ab/nsp31546L1546PcTtcCt11B.1.3690.000285
ORF1ab/nsp31546L1546FCttTtt11B.1.4270.00005
ORF1ab/nsp31546L1546PcTtcCt11B.1.4270.00005
ORF1ab/nsp31546L1546PcTtcCt11B.1.4280.00102
ORF1ab/nsp31546L1546FCttTtt11B.1.4290.000024
ORF1ab/nsp31546L1546LctTctC11B.1.4290.000024
ORF1ab/nsp31546L1546ICttAtt11B.1.438.10.000107
ORF1ab/nsp31546L1546FCttTtt11B.1.5250.000113
ORF1ab/nsp31546L1546delCTT---11B.1.5250.000113
ORF1ab/nsp31546L1546delCTT---11B.1.575.10.002439
ORF1ab/nsp31546L1546LctTctC11B.1.5950.000261
ORF1ab/nsp31546L1546ICttAtt11B.1.617.10.000129
ORF1ab/nsp31546L1546PcTtcCt11B.1.617.20.000004
ORF1ab/nsp31546L1546SCTTAGC11B.1.617.20.000004
ORF1ab/nsp31546L1546YCTtTAt11B.1.617.20.000004
ORF1ab/nsp31546L1546LctTctC11B.1.6210.000089
ORF1ab/nsp31546L1546delCTT---11B.1.6210.000089
ORF1ab/nsp31546L1546FCttTtt11B.1.6280.000352
ORF1ab/nsp31546L1546LctTctC11C.180.002591
ORF1ab/nsp31546L1546PcTTcCG11C.350.000774
ORF1ab/nsp31546L1546LctTctC11C.36.3.10.002717
ORF1ab/nsp31546L1546delCTT---11P.10.000016
ORF1ab/nsp31546L1546LctTctC11P.1.140.000048
ORF1ab/nsp31546L1546delCTT---11Q.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.