CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp2 : CodonNum = 303

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/nsp2303S303SS483SsyntcCtcT7487100.9491981712-1714
ORF1ab/nsp2303S303SS483SsyntcCtcA748360.04812831712-1714
ORF1ab/nsp2303S303SS483SsyntcCtcG74820.00267381712-1714
ORF1ab/nsp2303S303FS483FnonsyntCctTc17217211712-1714
ORF1ab/nsp2303S303PS483PnonsynTccCcc58550.9482761712-1714
ORF1ab/nsp2303S303PS483PnonsynTcCCcT5820.03448281712-1714
ORF1ab/nsp2303S303PS483PnonsynTcCCcA5810.01724141712-1714
ORF1ab/nsp2303S303delS483deldelTCC---474711712-1714
ORF1ab/nsp2303S303TS483TnonsynTccAcc35330.9428571712-1714
ORF1ab/nsp2303S303TS483TnonsynTcCAcA3520.05714291712-1714
ORF1ab/nsp2303S303YS483YnonsyntCctAc32300.93751712-1714
ORF1ab/nsp2303S303YS483YnonsyntCCtAT3220.06251712-1714
ORF1ab/nsp2303S303AS483AnonsynTccGcc30290.9666671712-1714
ORF1ab/nsp2303S303AS483AnonsynTcCGcA3010.03333331712-1714
ORF1ab/nsp2303S303HS483HnonsynTCcCAc530.61712-1714
ORF1ab/nsp2303S303HS483HnonsynTCCCAT520.41712-1714
ORF1ab/nsp2303S303CS483CnonsyntCctGc3311712-1714
ORF1ab/nsp2303S303del1S483del1delTcc-cc210.51712-1714
ORF1ab/nsp2303S303del1S483del1delTcCCc-210.51712-1714

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/nsp2303S303StcCtcT710748All0.000136
ORF1ab/nsp2303S303StcCtcA36748All0.000007
ORF1ab/nsp2303S303StcCtcG2748All0
ORF1ab/nsp2303S303FtCctTc172172All0.000033
ORF1ab/nsp2303S303StcCtcT98105B.1.1.70.000088
ORF1ab/nsp2303S303StcCtcA7105B.1.1.70.000006
ORF1ab/nsp2303S303StcCtcT9192AY.250.000547
ORF1ab/nsp2303S303StcCtcA192AY.250.000006
ORF1ab/nsp2303S303StcCtcT7575B.1.617.20.000282
ORF1ab/nsp2303S303FtCctTc6363B.1.1.70.000056
ORF1ab/nsp2303S303PTccCcc5558All0.000011
ORF1ab/nsp2303S303PTcCCcT258All0
ORF1ab/nsp2303S303PTcCCcA158All0
ORF1ab/nsp2303S303delTCC---4747All0.000009
ORF1ab/nsp2303S303StcCtcT4646AY.1020.00122
ORF1ab/nsp2303S303StcCtcT3838AY.40.000059
ORF1ab/nsp2303S303FtCctTc3636AY.260.001019
ORF1ab/nsp2303S303TTccAcc3335All0.000006
ORF1ab/nsp2303S303TTcCAcA235All0
ORF1ab/nsp2303S303YtCctAc3032All0.000006
ORF1ab/nsp2303S303YtCCtAT232All0
ORF1ab/nsp2303S303StcCtcT3131B.1.2311
ORF1ab/nsp2303S303ATccGcc2930All0.000006
ORF1ab/nsp2303S303ATcCGcA130All0
ORF1ab/nsp2303S303TTccAcc2727B.1.1.70.000024
ORF1ab/nsp2303S303StcCtcT1923AY.440.000116
ORF1ab/nsp2303S303StcCtcA323AY.440.000018
ORF1ab/nsp2303S303StcCtcG123AY.440.000006
ORF1ab/nsp2303S303StcCtcT2121B.1.3510.000624
ORF1ab/nsp2303S303StcCtcT1820AY.430.00008
ORF1ab/nsp2303S303StcCtcG120AY.430.000004
ORF1ab/nsp2303S303StcCtcA120AY.430.000004
ORF1ab/nsp2303S303PTccCcc1717AY.40.000026
ORF1ab/nsp2303S303StcCtcT1017B.1.1770.000132
ORF1ab/nsp2303S303StcCtcA717B.1.1770.000092
ORF1ab/nsp2303S303ATccGcc1717B.1.20.00015
ORF1ab/nsp2303S303StcCtcT1616AY.50.00033
ORF1ab/nsp2303S303PTccCcc1616B.1.1.70.000014
ORF1ab/nsp2303S303StcCtcT1515AY.1030.000093
ORF1ab/nsp2303S303StcCtcT1414AY.1000.000644
ORF1ab/nsp2303S303StcCtcT1012B.10.000092
ORF1ab/nsp2303S303StcCtcA212B.10.000018
ORF1ab/nsp2303S303delTCC---1212B.1.1.70.000011
ORF1ab/nsp2303S303StcCtcT1111AY.30.000109
ORF1ab/nsp2303S303FtCctTc1111AY.750.000616
ORF1ab/nsp2303S303StcCtcT1111P.10.000173
ORF1ab/nsp2303S303FtCctTc1010AY.40.000016
ORF1ab/nsp2303S303StcCtcT1010B.1.177.750.010406
ORF1ab/nsp2303S303StcCtcT89AY.390.000198
ORF1ab/nsp2303S303StcCtcA19AY.390.000025
ORF1ab/nsp2303S303StcCtcT88AY.90.000541
ORF1ab/nsp2303S303StcCtcT77AY.1100.000789
ORF1ab/nsp2303S303StcCtcT77AY.330.000467
ORF1ab/nsp2303S303StcCtcT77AY.530.002013
ORF1ab/nsp2303S303ATccGcc77B.1.1.70.000006
ORF1ab/nsp2303S303YtCctAc77B.1.2010.039773
ORF1ab/nsp2303S303YtCctAc460.222222
ORF1ab/nsp2303S303YtCCtAT260.111111
ORF1ab/nsp2303S303FtCctTc66AY.1020.000159
ORF1ab/nsp2303S303StcCtcA46AY.230.000279
ORF1ab/nsp2303S303StcCtcT26AY.230.000139
ORF1ab/nsp2303S303StcCtcT66AY.260.00017
ORF1ab/nsp2303S303StcCtcT56B.1.10.000091
ORF1ab/nsp2303S303StcCtcA16B.1.10.000018
ORF1ab/nsp2303S303StcCtcT66B.1.20.000053
ORF1ab/nsp2303S303StcCtcT66B.1.5260.000141
ORF1ab/nsp2303S303StcCtcT66B.1.5610.002382
ORF1ab/nsp2303S303FtCctTc66B.1.617.20.000023
ORF1ab/nsp2303S303HTCcCAc35All0.000001
ORF1ab/nsp2303S303HTCCCAT25All0
ORF1ab/nsp2303S303StcCtcT55AY.4.20.000108
ORF1ab/nsp2303S303StcCtcT55AY.9.10.000419
ORF1ab/nsp2303S303PTccCcc240.111111
ORF1ab/nsp2303S303PTcCCcT240.111111
ORF1ab/nsp2303S303HTCCCAT240.111111
ORF1ab/nsp2303S303HTCcCAc240.111111
ORF1ab/nsp2303S303StcCtcT44AY.1200.000149
ORF1ab/nsp2303S303StcCtcT44AY.120.10.001284
ORF1ab/nsp2303S303StcCtcT44AY.890.019608
ORF1ab/nsp2303S303FtCctTc44B.10.000037
ORF1ab/nsp2303S303delTCC---44B.1.1.330.001684
ORF1ab/nsp2303S303delTCC---44B.1.1770.000053
ORF1ab/nsp2303S303FtCctTc44B.1.20.000035
ORF1ab/nsp2303S303FtCctTc44P.10.000063
ORF1ab/nsp2303S303CtCctGc33All0.000001
ORF1ab/nsp2303S303FtCctTc33AY.1160.00086
ORF1ab/nsp2303S303StcCtcT33AY.1180.000188
ORF1ab/nsp2303S303delTCC---33AY.40.000005
ORF1ab/nsp2303S303StcCtcT33AY.450.000365
ORF1ab/nsp2303S303StcCtcT33AY.980.000237
ORF1ab/nsp2303S303PTccCcc33B.10.000027
ORF1ab/nsp2303S303delTCC---33B.1.1.3480.002389
ORF1ab/nsp2303S303StcCtcA33B.1.3190.009146
ORF1ab/nsp2303S303delTCC---33B.1.617.20.000011
ORF1ab/nsp2303S303StcCtcT33C.360.002732
ORF1ab/nsp2303S303StcCtcT33R.10.00027
ORF1ab/nsp2303S303TTcCAcA220.111111
ORF1ab/nsp2303S303CtCctGc220.111111
ORF1ab/nsp2303S303StcCtcT220.111111
ORF1ab/nsp2303S303StcCtcT12A0.000387
ORF1ab/nsp2303S303StcCtcA12A0.000387
ORF1ab/nsp2303S303del1Tcc-cc12All0
ORF1ab/nsp2303S303del1TcCCc-12All0
ORF1ab/nsp2303S303FtCctTc22AY.1030.000012
ORF1ab/nsp2303S303FtCctTc22AY.250.000012
ORF1ab/nsp2303S303StcCtcT22AY.270.000129
ORF1ab/nsp2303S303StcCtcT22AY.340.000194
ORF1ab/nsp2303S303StcCtcT22AY.39.10.000079
ORF1ab/nsp2303S303YtCctAc22AY.400.001929
ORF1ab/nsp2303S303FtCctTc22AY.420.00008
ORF1ab/nsp2303S303YtCctAc22AY.46.60.000144
ORF1ab/nsp2303S303StcCtcT22AY.470.000062
ORF1ab/nsp2303S303StcCtcT22AY.580.001815
ORF1ab/nsp2303S303YtCctAc22AY.860.00166
ORF1ab/nsp2303S303StcCtcT22AY.9.20.000073
ORF1ab/nsp2303S303StcCtcT22AY.9.2.10.003953
ORF1ab/nsp2303S303YtCctAc22B.1.1.70.000002
ORF1ab/nsp2303S303StcCtcT22B.1.177.120.000303
ORF1ab/nsp2303S303PTccCcc22B.1.20.000018
ORF1ab/nsp2303S303StcCtcA22B.1.2210.000142
ORF1ab/nsp2303S303FtCctTc22B.1.3750.001639
ORF1ab/nsp2303S303PTccCcc22B.1.4170.057143
ORF1ab/nsp2303S303StcCtcT22B.1.5960.000174
ORF1ab/nsp2303S303StcCtcT22B.1.6370.000146
ORF1ab/nsp2303S303StcCtcT22B.30.001661
ORF1ab/nsp2303S303delTCC---22N.60.014184
ORF1ab/nsp2303S303StcCtcT22P.1.140.000096
ORF1ab/nsp2303S303delTCC---22P.20.000373
ORF1ab/nsp2303S303StcCtcT22Q.30.00029
ORF1ab/nsp2303S303StcCtcT22Q.80.00033
ORF1ab/nsp2303S303delTCC---11A0.000387
ORF1ab/nsp2303S303StcCtcT11A.2.50.000499
ORF1ab/nsp2303S303FtCctTc11A.2.5.10.004808
ORF1ab/nsp2303S303StcCtcT11AD.20.000219
ORF1ab/nsp2303S303StcCtcT11AY.100.00053
ORF1ab/nsp2303S303PTccCcc11AY.1030.000006
ORF1ab/nsp2303S303StcCtcT11AY.1130.000142
ORF1ab/nsp2303S303delTCC---11AY.1130.000142
ORF1ab/nsp2303S303delTCC---11AY.1190.000035
ORF1ab/nsp2303S303StcCtcT11AY.1190.000035
ORF1ab/nsp2303S303StcCtcT11AY.120.000316
ORF1ab/nsp2303S303FtCctTc11AY.1200.000037
ORF1ab/nsp2303S303StcCtcT11AY.1210.000135
ORF1ab/nsp2303S303FtCctTc11AY.130.000161
ORF1ab/nsp2303S303TTccAcc11AY.160.00038
ORF1ab/nsp2303S303TTccAcc11AY.190.00114
ORF1ab/nsp2303S303YtCctAc11AY.230.00007
ORF1ab/nsp2303S303TTccAcc11AY.250.000006
ORF1ab/nsp2303S303ATccGcc11AY.260.000028
ORF1ab/nsp2303S303FtCctTc11AY.290.000016
ORF1ab/nsp2303S303StcCtcT11AY.290.000016
ORF1ab/nsp2303S303delTCC---11AY.290.000016
ORF1ab/nsp2303S303delTCC---11AY.30.00001
ORF1ab/nsp2303S303FtCctTc11AY.300.000396
ORF1ab/nsp2303S303FtCctTc11AY.330.000067
ORF1ab/nsp2303S303FtCctTc11AY.34.10.00051
ORF1ab/nsp2303S303StcCtcT11AY.350.000233
ORF1ab/nsp2303S303ATccGcc11AY.390.000025
ORF1ab/nsp2303S303YtCctAc11AY.390.000025
ORF1ab/nsp2303S303ATccGcc11AY.40.000002
ORF1ab/nsp2303S303StcCtcT11AY.4.10.000737
ORF1ab/nsp2303S303delTCC---11AY.4.50.000107
ORF1ab/nsp2303S303StcCtcT11AY.420.00004
ORF1ab/nsp2303S303del1TcCCc-11AY.430.000004
ORF1ab/nsp2303S303FtCctTc11AY.430.000004
ORF1ab/nsp2303S303HTCcCAc11AY.440.000006
ORF1ab/nsp2303S303StcCtcA11AY.460.000104
ORF1ab/nsp2303S303FtCctTc11AY.46.20.000635
ORF1ab/nsp2303S303StcCtcT11AY.5.30.000337
ORF1ab/nsp2303S303StcCtcT11AY.5.40.000277
ORF1ab/nsp2303S303delTCC---11AY.670.000464
ORF1ab/nsp2303S303StcCtcT11AY.700.000209
ORF1ab/nsp2303S303StcCtcT11AY.730.000665
ORF1ab/nsp2303S303StcCtcT11AY.740.000116
ORF1ab/nsp2303S303StcCtcT11AY.750.000056
ORF1ab/nsp2303S303YtCctAc11AY.75.10.00018
ORF1ab/nsp2303S303PTccCcc11AY.75.10.00018
ORF1ab/nsp2303S303StcCtcT11AY.840.000437
ORF1ab/nsp2303S303YtCctAc11AY.9.20.000037
ORF1ab/nsp2303S303FtCctTc11AY.9.20.000037
ORF1ab/nsp2303S303delTCC---11AY.990.001049
ORF1ab/nsp2303S303StcCtcT11AY.990.001049
ORF1ab/nsp2303S303StcCtcA11AY.99.10.001553
ORF1ab/nsp2303S303YtCctAc11AY.99.20.000092
ORF1ab/nsp2303S303YtCctAc11B.10.000009
ORF1ab/nsp2303S303TTccAcc11B.10.000009
ORF1ab/nsp2303S303ATcCGcA11B.1.10.000018
ORF1ab/nsp2303S303FtCctTc11B.1.10.000018
ORF1ab/nsp2303S303CtCctGc11B.1.10.000018
ORF1ab/nsp2303S303StcCtcT11B.1.1.2140.000055
ORF1ab/nsp2303S303StcCtcT11B.1.1.2160.00089
ORF1ab/nsp2303S303delTCC---11B.1.1.2840.000107
ORF1ab/nsp2303S303StcCtcT11B.1.1.3010.001179
ORF1ab/nsp2303S303PTccCcc11B.1.1.3110.000358
ORF1ab/nsp2303S303StcCtcT11B.1.1.3180.000302
ORF1ab/nsp2303S303PTccCcc11B.1.1.3690.000446
ORF1ab/nsp2303S303StcCtcT11B.1.1.4320.001266
ORF1ab/nsp2303S303del1Tcc-cc11B.1.1.70.000001
ORF1ab/nsp2303S303StcCtcT11B.1.110.30.000718
ORF1ab/nsp2303S303FtCctTc11B.1.1460.004237
ORF1ab/nsp2303S303StcCtcT11B.1.1600.000031
ORF1ab/nsp2303S303PTccCcc11B.1.1600.000031
ORF1ab/nsp2303S303StcCtcT11B.1.160.260.002421
ORF1ab/nsp2303S303PTccCcc11B.1.160.290.004219
ORF1ab/nsp2303S303PTccCcc11B.1.160.90.007194
ORF1ab/nsp2303S303YtCctAc11B.1.1770.000013
ORF1ab/nsp2303S303PTccCcc11B.1.1770.000013
ORF1ab/nsp2303S303delTCC---11B.1.177.160.000664
ORF1ab/nsp2303S303delTCC---11B.1.177.40.000211
ORF1ab/nsp2303S303YtCctAc11B.1.177.440.000519
ORF1ab/nsp2303S303StcCtcT11B.1.177.440.000519
ORF1ab/nsp2303S303StcCtcT11B.1.177.460.000918
ORF1ab/nsp2303S303delTCC---11B.1.177.570.000281
ORF1ab/nsp2303S303ATccGcc11B.1.2410.000812
ORF1ab/nsp2303S303StcCtcT11B.1.2430.00007
ORF1ab/nsp2303S303FtCctTc11B.1.2580.000067
ORF1ab/nsp2303S303StcCtcT11B.1.2580.000067
ORF1ab/nsp2303S303YtCctAc11B.1.3110.000275
ORF1ab/nsp2303S303FtCctTc11B.1.3490.000715
ORF1ab/nsp2303S303TTccAcc11B.1.3510.00003
ORF1ab/nsp2303S303ATccGcc11B.1.3510.00003
ORF1ab/nsp2303S303StcCtcT11B.1.351.50.0006
ORF1ab/nsp2303S303StcCtcT11B.1.36.180.00042
ORF1ab/nsp2303S303delTCC---11B.1.36.240.006173
ORF1ab/nsp2303S303StcCtcT11B.1.36.310.001751
ORF1ab/nsp2303S303FtCctTc11B.1.4270.00005
ORF1ab/nsp2303S303StcCtcT11B.1.4290.000024
ORF1ab/nsp2303S303YtCctAc11B.1.4740.001901
ORF1ab/nsp2303S303delTCC---11B.1.5250.000113
ORF1ab/nsp2303S303FtCctTc11B.1.5260.000024
ORF1ab/nsp2303S303PTccCcc11B.1.5950.000261
ORF1ab/nsp2303S303YtCctAc11B.1.617.20.000004
ORF1ab/nsp2303S303StcCtcT11B.1.617.30.002985
ORF1ab/nsp2303S303StcCtcT11B.1.6200.000946
ORF1ab/nsp2303S303StcCtcT11B.1.6210.000089
ORF1ab/nsp2303S303TTccAcc11B.1.6210.000089
ORF1ab/nsp2303S303StcCtcA11B.1.6280.000352
ORF1ab/nsp2303S303PTccCcc11B.390.002331
ORF1ab/nsp2303S303PTccCcc11D.20.000075
ORF1ab/nsp2303S303PTcCCcA11L.30.003546
ORF1ab/nsp2303S303PTccCcc11P.1.10.000318
ORF1ab/nsp2303S303PTccCcc11P.1.150.000232
ORF1ab/nsp2303S303StcCtcT11P.60.003145
ORF1ab/nsp2303S303FtCctTc11Q.10.000126
ORF1ab/nsp2303S303StcCtcT11Z.10.00289

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.