CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 612

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/nsp12612P612PP5004PsynccTccA501046010.91836315274-15276
ORF1ab/nsp12612P612PP5004PsynccTccC50103360.067065915274-15276
ORF1ab/nsp12612P612PP5004PsynccTccG5010730.014570915274-15276
ORF1ab/nsp12612P612SP5004SnonsynCctTct2062050.99514615274-15276
ORF1ab/nsp12612P612SP5004SnonsynCCtAGt20610.0048543715274-15276
ORF1ab/nsp12612P612delP5004deldelCCT---3131115274-15276
ORF1ab/nsp12612P612HP5004HnonsyncCtcAt21200.95238115274-15276
ORF1ab/nsp12612P612HP5004HnonsyncCTcAC2110.04761915274-15276
ORF1ab/nsp12612P612TP5004TnonsynCctAct55115274-15276
ORF1ab/nsp12612P612LP5004LnonsyncCtcTt430.7515274-15276
ORF1ab/nsp12612P612LP5004LnonsynCCTTTA410.2515274-15276
ORF1ab/nsp12612P612RP5004RnonsyncCtcGt22115274-15276
ORF1ab/nsp12612P612del1P5004del1delccTcc-11115274-15276
ORF1ab/nsp12612P612CP5004CnonsynCCtTGt11115274-15276
ORF1ab/nsp12612P612del2P5004del2delCCT--C11115274-15276

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/nsp12612P612PccTccA46015010All0.00088
ORF1ab/nsp12612P612PccTccC3365010All0.000064
ORF1ab/nsp12612P612PccTccG735010All0.000014
ORF1ab/nsp12612P612PccTccA19411941B.1.5820.952404
ORF1ab/nsp12612P612PccTccA10491054B.10.009608
ORF1ab/nsp12612P612PccTccC41054B.10.000037
ORF1ab/nsp12612P612PccTccG11054B.10.000009
ORF1ab/nsp12612P612PccTccA846846B.1.5680.94
ORF1ab/nsp12612P612PccTccA375375B.1.6120.994695
ORF1ab/nsp12612P612SCctTct205206All0.000039
ORF1ab/nsp12612P612SCCtAGt1206All0
ORF1ab/nsp12612P612PccTccA100100B.1.5810.943396
ORF1ab/nsp12612P612PccTccA8696B.1.20.000757
ORF1ab/nsp12612P612PccTccC696B.1.20.000053
ORF1ab/nsp12612P612PccTccG496B.1.20.000035
ORF1ab/nsp12612P612PccTccC4964AY.40.000076
ORF1ab/nsp12612P612PccTccA1064AY.40.000016
ORF1ab/nsp12612P612PccTccG564AY.40.000008
ORF1ab/nsp12612P612PccTccC4646B.1.5260.001081
ORF1ab/nsp12612P612PccTccC3245B.1.1.70.000029
ORF1ab/nsp12612P612PccTccG1345B.1.1.70.000012
ORF1ab/nsp12612P612SCctTct4444AY.40.000068
ORF1ab/nsp12612P612PccTccA4444B.1.5960.003834
ORF1ab/nsp12612P612SCctTct3232AY.1030.000199
ORF1ab/nsp12612P612delCCT---3131All0.000006
ORF1ab/nsp12612P612PccTccC2727AY.410.007937
ORF1ab/nsp12612P612PccTccG1727B.1.617.20.000064
ORF1ab/nsp12612P612PccTccC927B.1.617.20.000034
ORF1ab/nsp12612P612PccTccA127B.1.617.20.000004
ORF1ab/nsp12612P612PccTccC2525AY.140.0022
ORF1ab/nsp12612P612PccTccC2325AY.250.000138
ORF1ab/nsp12612P612PccTccG125AY.250.000006
ORF1ab/nsp12612P612PccTccA125AY.250.000006
ORF1ab/nsp12612P612SCctTct2222B.1.617.20.000083
ORF1ab/nsp12612P612HcCtcAt2021All0.000004
ORF1ab/nsp12612P612HcCTcAC121All0
ORF1ab/nsp12612P612PccTccC1818B.1.1.3060.007891
ORF1ab/nsp12612P612PccTccA1516B.1.10.000272
ORF1ab/nsp12612P612PccTccC116B.1.10.000018
ORF1ab/nsp12612P612PccTccG1414AY.1000.000644
ORF1ab/nsp12612P612SCctTct1414AY.390.000346
ORF1ab/nsp12612P612PccTccC1314AY.440.000079
ORF1ab/nsp12612P612PccTccA114AY.440.000006
ORF1ab/nsp12612P612delCCT---1414B.1.1.70.000013
ORF1ab/nsp12612P612PccTccA1212B.1.1.3500.48
ORF1ab/nsp12612P612PccTccA1212B.1.5170.005124
ORF1ab/nsp12612P612SCctTct1111AY.200.000428
ORF1ab/nsp12612P612SCctTct1111AY.30.000109
ORF1ab/nsp12612P612SCctTct1111AY.330.000735
ORF1ab/nsp12612P612SCctTct1010AY.250.00006
ORF1ab/nsp12612P612PccTccC88AY.430.000035
ORF1ab/nsp12612P612PccTccA88B.1.3690.002282
ORF1ab/nsp12612P612PccTccC88B.1.6130.216216
ORF1ab/nsp12612P612PccTccC88P.10.000126
ORF1ab/nsp12612P612HcCtcAt77AY.40.000011
ORF1ab/nsp12612P612PccTccA77B.1.5760.006346
ORF1ab/nsp12612P612PccTccG66AY.390.000148
ORF1ab/nsp12612P612SCctTct66AY.430.000027
ORF1ab/nsp12612P612SCctTct56B.1.1.70.000004
ORF1ab/nsp12612P612SCCtAGt16B.1.1.70.000001
ORF1ab/nsp12612P612PccTccC56B.1.1770.000066
ORF1ab/nsp12612P612PccTccA16B.1.1770.000013
ORF1ab/nsp12612P612PccTccA66B.1.4510.04918
ORF1ab/nsp12612P612PccTccA66B.1.5640.002555
ORF1ab/nsp12612P612TCctAct55All0.000001
ORF1ab/nsp12612P612PccTccC45AY.260.000113
ORF1ab/nsp12612P612PccTccA15AY.260.000028
ORF1ab/nsp12612P612SCctTct55AY.440.00003
ORF1ab/nsp12612P612PccTccA55B.1.2060.004078
ORF1ab/nsp12612P612PccTccA55B.1.5800.020325
ORF1ab/nsp12612P612LcCtcTt34All0.000001
ORF1ab/nsp12612P612LCCTTTA14All0
ORF1ab/nsp12612P612SCctTct44AY.4.50.00043
ORF1ab/nsp12612P612PccTccA44AY.4.50.00043
ORF1ab/nsp12612P612SCctTct44AY.60.000165
ORF1ab/nsp12612P612PccTccA44B.1.1.4320.005063
ORF1ab/nsp12612P612PccTccA44B.1.2840.052632
ORF1ab/nsp12612P612PccTccC34B.1.466.20.001174
ORF1ab/nsp12612P612PccTccA14B.1.466.20.000391
ORF1ab/nsp12612P612PccTccA44B.1.5770.002749
ORF1ab/nsp12612P612PccTccA44B.1.5950.001044
ORF1ab/nsp12612P612SCctTct33AY.1020.00008
ORF1ab/nsp12612P612PccTccG33AY.1170.000254
ORF1ab/nsp12612P612HcCtcAt33B.10.000027
ORF1ab/nsp12612P612PccTccC33B.1.1.2840.000322
ORF1ab/nsp12612P612PccTccA23B.1.2340.000264
ORF1ab/nsp12612P612PccTccC13B.1.2340.000132
ORF1ab/nsp12612P612PccTccA33B.1.36.220.003623
ORF1ab/nsp12612P612PccTccA33B.1.3960.002117
ORF1ab/nsp12612P612PccTccC33B.1.5380.024194
ORF1ab/nsp12612P612PccTccC33B.1.5650.002431
ORF1ab/nsp12612P612RcCtcGt22All0
ORF1ab/nsp12612P612PccTccG12AY.1030.000006
ORF1ab/nsp12612P612PccTccC12AY.1030.000006
ORF1ab/nsp12612P612SCctTct22AY.230.000139
ORF1ab/nsp12612P612PccTccC22AY.270.000129
ORF1ab/nsp12612P612PccTccC22AY.290.000032
ORF1ab/nsp12612P612PccTccC22AY.30.00002
ORF1ab/nsp12612P612SCctTct22AY.50.000041
ORF1ab/nsp12612P612SCctTct22AY.70.000392
ORF1ab/nsp12612P612PccTccC22AY.750.000112
ORF1ab/nsp12612P612PccTccC12AY.90.000068
ORF1ab/nsp12612P612PccTccA12AY.90.000068
ORF1ab/nsp12612P612PccTccC22AY.99.20.000184
ORF1ab/nsp12612P612SCctTct22B.10.000018
ORF1ab/nsp12612P612PccTccA22B.1.1.2580.006515
ORF1ab/nsp12612P612PccTccA22B.1.1.3350.025974
ORF1ab/nsp12612P612HcCtcAt12B.1.1.70.000001
ORF1ab/nsp12612P612HcCTcAC12B.1.1.70.000001
ORF1ab/nsp12612P612PccTccA22B.1.1390.001466
ORF1ab/nsp12612P612PccTccA22B.1.177.650.001331
ORF1ab/nsp12612P612PccTccG12B.1.2400.000216
ORF1ab/nsp12612P612PccTccA12B.1.2400.000216
ORF1ab/nsp12612P612PccTccA22B.1.2430.000139
ORF1ab/nsp12612P612PccTccG12B.1.3510.00003
ORF1ab/nsp12612P612PccTccC12B.1.3510.00003
ORF1ab/nsp12612P612PccTccA22B.1.3670.001585
ORF1ab/nsp12612P612PccTccA22B.1.5210.00995
ORF1ab/nsp12612P612PccTccA22B.1.5460.007407
ORF1ab/nsp12612P612PccTccA22B.1.6060.012048
ORF1ab/nsp12612P612PccTccC22B.1.6230.001073
ORF1ab/nsp12612P612SCctTct11A.2.30.004739
ORF1ab/nsp12612P612PccTccC11A.50.001923
ORF1ab/nsp12612P612delCCT---11AD.20.000219
ORF1ab/nsp12612P612SCctTct11AK.10.012658
ORF1ab/nsp12612P612del1ccTcc-11All0
ORF1ab/nsp12612P612del2CCT--C11All0
ORF1ab/nsp12612P612CCCtTGt11All0
ORF1ab/nsp12612P612PccTccC11AM.30.033333
ORF1ab/nsp12612P612PccTccG11AY.1020.000027
ORF1ab/nsp12612P612PccTccC11AY.1090.00074
ORF1ab/nsp12612P612SCctTct11AY.1130.000142
ORF1ab/nsp12612P612PccTccC11AY.1160.000287
ORF1ab/nsp12612P612PccTccC11AY.1190.000035
ORF1ab/nsp12612P612HcCtcAt11AY.1200.000037
ORF1ab/nsp12612P612PccTccG11AY.120.10.000321
ORF1ab/nsp12612P612PccTccC11AY.160.00038
ORF1ab/nsp12612P612PccTccC11AY.230.00007
ORF1ab/nsp12612P612HcCtcAt11AY.240.000431
ORF1ab/nsp12612P612PccTccA11AY.240.000431
ORF1ab/nsp12612P612delCCT---11AY.250.000006
ORF1ab/nsp12612P612SCctTct11AY.260.000028
ORF1ab/nsp12612P612SCctTct11AY.3.10.000085
ORF1ab/nsp12612P612delCCT---11AY.340.000097
ORF1ab/nsp12612P612TCctAct11AY.390.000025
ORF1ab/nsp12612P612SCctTct11AY.4.20.000022
ORF1ab/nsp12612P612HcCtcAt11AY.4.20.000022
ORF1ab/nsp12612P612delCCT---11AY.4.50.000107
ORF1ab/nsp12612P612PccTccC11AY.420.00004
ORF1ab/nsp12612P612delCCT---11AY.430.000004
ORF1ab/nsp12612P612del2CCT--C11AY.440.000006
ORF1ab/nsp12612P612PccTccG11AY.46.60.000072
ORF1ab/nsp12612P612LcCtcTt11AY.50.000021
ORF1ab/nsp12612P612SCctTct11AY.510.000909
ORF1ab/nsp12612P612PccTccC11AY.540.000095
ORF1ab/nsp12612P612SCctTct11AY.540.000095
ORF1ab/nsp12612P612HcCtcAt11AY.60.000041
ORF1ab/nsp12612P612PccTccG11AY.610.000105
ORF1ab/nsp12612P612SCctTct11AY.750.000056
ORF1ab/nsp12612P612delCCT---11AY.75.10.00018
ORF1ab/nsp12612P612PccTccC11AY.9.20.000037
ORF1ab/nsp12612P612PccTccC11AY.98.10.000048
ORF1ab/nsp12612P612SCctTct11AY.99.20.000092
ORF1ab/nsp12612P612HcCtcAt11B0.000128
ORF1ab/nsp12612P612PccTccC11B0.000128
ORF1ab/nsp12612P612TCctAct11B.10.000009
ORF1ab/nsp12612P612SCctTct11B.1.10.000018
ORF1ab/nsp12612P612RcCtcGt11B.1.10.000018
ORF1ab/nsp12612P612CCCtTGt11B.1.10.000018
ORF1ab/nsp12612P612PccTccA11B.1.1.2100.005714
ORF1ab/nsp12612P612PccTccA11B.1.1.2260.005814
ORF1ab/nsp12612P612PccTccA11B.1.1.2300.009174
ORF1ab/nsp12612P612PccTccA11B.1.1.4660.008696
ORF1ab/nsp12612P612TCctAct11B.1.1.70.000001
ORF1ab/nsp12612P612LcCtcTt11B.1.1.70.000001
ORF1ab/nsp12612P612delCCT---11B.1.1.700.000341
ORF1ab/nsp12612P612HcCtcAt11B.1.1.700.000341
ORF1ab/nsp12612P612SCctTct11B.1.1.980.018519
ORF1ab/nsp12612P612delCCT---11B.1.1400.018868
ORF1ab/nsp12612P612delCCT---11B.1.160.230.004831
ORF1ab/nsp12612P612HcCtcAt11B.1.1770.000013
ORF1ab/nsp12612P612delCCT---11B.1.1770.000013
ORF1ab/nsp12612P612PccTccC11B.1.177.120.000152
ORF1ab/nsp12612P612delCCT---11B.1.177.160.000664
ORF1ab/nsp12612P612PccTccC11B.1.177.40.000211
ORF1ab/nsp12612P612PccTccG11B.1.177.440.000519
ORF1ab/nsp12612P612delCCT---11B.1.177.50.001242
ORF1ab/nsp12612P612delCCT---11B.1.177.540.000606
ORF1ab/nsp12612P612delCCT---11B.1.177.90.001332
ORF1ab/nsp12612P612del1ccTcc-11B.1.20.000009
ORF1ab/nsp12612P612SCctTct11B.1.20.000009
ORF1ab/nsp12612P612LcCtcTt11B.1.20.000009
ORF1ab/nsp12612P612PccTccC11B.1.2210.000071
ORF1ab/nsp12612P612PccTccA11B.1.2320.000537
ORF1ab/nsp12612P612PccTccA11B.1.3050.002151
ORF1ab/nsp12612P612PccTccC11B.1.3240.001605
ORF1ab/nsp12612P612PccTccA11B.1.3360.002439
ORF1ab/nsp12612P612PccTccA11B.1.3500.002933
ORF1ab/nsp12612P612PccTccA11B.1.3610.001289
ORF1ab/nsp12612P612PccTccA11B.1.3630.012987
ORF1ab/nsp12612P612PccTccA11B.1.3700.008
ORF1ab/nsp12612P612PccTccG11B.1.3890.001002
ORF1ab/nsp12612P612delCCT---11B.1.4150.014286
ORF1ab/nsp12612P612PccTccA11B.1.4240.008065
ORF1ab/nsp12612P612PccTccA11B.1.4430.004673
ORF1ab/nsp12612P612PccTccC11B.1.4690.00361
ORF1ab/nsp12612P612TCctAct11B.1.4700.001404
ORF1ab/nsp12612P612PccTccC11B.1.5090.000866
ORF1ab/nsp12612P612PccTccA11B.1.5660.019231
ORF1ab/nsp12612P612PccTccA11B.1.5870.001898
ORF1ab/nsp12612P612PccTccA11B.1.5890.007576
ORF1ab/nsp12612P612LCCTTTA11B.1.617.10.000129
ORF1ab/nsp12612P612delCCT---11B.1.617.20.000004
ORF1ab/nsp12612P612TCctAct11B.1.617.20.000004
ORF1ab/nsp12612P612SCctTct11B.1.6210.000089
ORF1ab/nsp12612P612PccTccA11B.1.6270.00202
ORF1ab/nsp12612P612PccTccA11B.1.6340.003425
ORF1ab/nsp12612P612HcCtcAt11B.60.00091
ORF1ab/nsp12612P612HcCtcAt11B.6.60.000889
ORF1ab/nsp12612P612PccTccA11C.370.000116
ORF1ab/nsp12612P612RcCtcGt11D.20.000075
ORF1ab/nsp12612P612PccTccC11P.1.150.000232
ORF1ab/nsp12612P612PccTccC11P.1.170.000162
ORF1ab/nsp12612P612PccTccC11P.1.40.000977
ORF1ab/nsp12612P612PccTccC11P.20.000187
ORF1ab/nsp12612P612SCctTct11P.20.000187
ORF1ab/nsp12612P612delCCT---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.