CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = S : CodonNum = 249

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
S249L249deldelTTG---77827782122307-22309
S249L249SnonsyntTgtCg8558380.98011722307-22309
S249L249SnonsyntTGtCA855120.014035122307-22309
S249L249SnonsyntTGtCT85550.0058479522307-22309
S249L249LsynTtgCtg4072640.64864922307-22309
S249L249LsynttGttA4071390.34152322307-22309
S249L249LsynTtGCtA40720.00491422307-22309
S249L249LsynTtGCtT40720.00491422307-22309
S249L249FnonsynttGttT2542490.98031522307-22309
S249L249FnonsynttGttC25450.01968522307-22309
S249L249VnonsynTtgGtg6363122307-22309
S249L249WnonsyntTgtGg2424122307-22309
S249L249MnonsynTtgAtg1717122307-22309
S249L249del2delTTg--g530.622307-22309
S249L249del2deltTGt--520.422307-22309
S249L249PnonsynTTGCCT420.522307-22309
S249L249PnonsynTTGCCA420.522307-22309
S249L249XnonsyntTgtAg22122307-22309
S249L249EnonsynTTgGAg11122307-22309
S249L249del1delTTG-NN11122307-22309
S249L249InonsynTtGAtA11122307-22309

Details of the mutation no within lineages (LineageCodonProp is the proportion the codon is observed at, at this particular site, on each lineage):

ORFCodonNumMutRefCodonMutCodonCodonCountAACountLineageLineageCodonProp
S249L249delTTG---77827782All0.001488
S249L249delTTG---74027402C.370.859099
S249L249StTgtCg838855All0.00016
S249L249StTGtCA12855All0.000002
S249L249StTGtCT5855All0.000001
S249L249StTgtCg541541B.1.20.004764
S249L249LTtgCtg264407All0.00005
S249L249LttGttA139407All0.000027
S249L249LTtGCtT2407All0
S249L249LTtGCtA2407All0
S249L249delTTG---267267C.37.10.698953
S249L249FttGttT249254All0.000048
S249L249FttGttC5254All0.000001
S249L249StTgtCg108108B.10.000989
S249L249LTtgCtg8290AY.430.000363
S249L249LttGttA890AY.430.000035
S249L249LTtgCtg7277B.1.617.20.000271
S249L249LttGttA577B.1.617.20.000019
S249L249StTgtCg6767B.1.1600.00209
S249L249VTtgGtg6363All0.000012
S249L249VTtgGtg5252B.1.1.70.000047
S249L249LTtgCtg3636C.350.027864
S249L249FttGttT3334B.1.1.70.00003
S249L249FttGttC134B.1.1.70.000001
S249L249FttGttT3232AY.40.00005
S249L249FttGttT2828AY.4.20.000607
S249L249LTtgCtg2626B.1.10.000472
S249L249LttGttA2626B.1.400.509804
S249L249WtTgtGg2424All0.000005
S249L249LttGttA1919AY.140.001672
S249L249StTgtCg1818AY.440.00011
S249L249LttGttA918B.1.1.70.000008
S249L249LTtgCtg918B.1.1.70.000008
S249L249StTGtCA1218C.370.001393
S249L249StTGtCT518C.370.00058
S249L249StTgtCg118C.370.000116
S249L249delTTG---1818P.1.150.004182
S249L249MTtgAtg1717All0.000003
S249L249FttGttT1616B.1.617.20.00006
S249L249delTTG---1515B.1.1.70.000013
S249L249FttGttT1313AY.250.000078
S249L249FttGttT1313B.1.1770.000171
S249L249WtTgtGg1212AY.430.000053
S249L249FttGttT1111AY.30.000109
S249L249StTgtCg1111B.1.10.0002
S249L249StTgtCg1111B.1.1.70.00001
S249L249delTTG---99B.10.000082
S249L249StTgtCg99B.1.4290.000212
S249L249LttGttA59C.370.00058
S249L249LTtGCtT29C.370.000232
S249L249LTtGCtA29C.370.000232
S249L249LttGttA58AY.390.000124
S249L249LTtgCtg38AY.390.000074
S249L249FttGttT88AY.440.000049
S249L249FttGttT77AY.1020.000186
S249L249LTtgCtg77AY.1160.002007
S249L249LttGttA77AY.250.000042
S249L249FttGttT77AY.290.00011
S249L249delTTG---77AY.430.000031
S249L249StTgtCg77B.1.1110.008226
S249L249StTgtCg77B.1.2580.000466
S249L249MTtgAtg77B.1.4290.000165
S249L249StTgtCg77B.1.5680.007778
S249L249FttGttT66AY.130.000966
S249L249StTgtCg66AY.40.000009
S249L249LttGttA46AY.440.000024
S249L249LTtgCtg26AY.440.000012
S249L249LttGttA66AY.46.60.000433
S249L249FttGttT66B.10.000055
S249L249delTTG---66P.10.000095
S249L249MTtgAtg55A.300.714286
S249L249del2TTg--g35All0.000001
S249L249del2tTGt--25All0
S249L249FttGttT55AY.4.50.000537
S249L249FttGttT55AY.430.000022
S249L249StTgtCg55B.1.5250.000566
S249L249delTTG---55B.1.617.20.000019
S249L249delTTG---55B.1.6210.000443
S249L249FttGttT55C.370.00058
S249L249LttGttA55P.10.000079
S249L249StTgtCg55P.20.000933
S249L249PTTGCCT24All0
S249L249PTTGCCA24All0
S249L249FttGttT44AY.1030.000025
S249L249LttGttA34AY.1210.000406
S249L249LTtgCtg14AY.1210.000135
S249L249delTTG---44AY.250.000024
S249L249delTTG---44AY.290.000063
S249L249LttGttA44AY.40.000006
S249L249FttGttT44AY.46.60.000289
S249L249FttGttT34B.1.10.000054
S249L249FttGttC14B.1.10.000018
S249L249FttGttT44B.1.20.000035
S249L249StTgtCg44B.1.2430.000278
S249L249FttGttT44B.1.3510.000119
S249L249StTgtCg44B.1.617.20.000015
S249L249PTTGCCA24C.370.000232
S249L249PTTGCCT24C.370.000232
S249L249delTTG---33AY.1020.00008
S249L249LTtgCtg33AY.1150.015625
S249L249LttGttA33AY.260.000085
S249L249delTTG---33AY.4.50.000322
S249L249FttGttT33AY.420.000121
S249L249FttGttT33B0.000383
S249L249VTtgGtg33B.10.000027
S249L249WtTgtGg33B.1.1.70.000003
S249L249delTTG---33B.1.1770.00004
S249L249LTtgCtg33B.1.177.330.004934
S249L249LTtgCtg23B.1.20.000018
S249L249LttGttA13B.1.20.000009
S249L249LttGttA33B.1.258.170.000312
S249L249FttGttT33B.1.4260.003027
S249L249delTTG---220.111111
S249L249XtTgtAg22All0
S249L249FttGttT22AY.1000.000092
S249L249LTtgCtg12AY.1030.000006
S249L249LttGttA12AY.1030.000006
S249L249LTtgCtg22AY.1140.000462
S249L249LTtgCtg12AY.1180.000063
S249L249LttGttA12AY.1180.000063
S249L249LTtgCtg22AY.1190.000071
S249L249delTTG---22AY.440.000012
S249L249LTtgCtg22AY.50.000041
S249L249LttGttA12AY.540.000095
S249L249LTtgCtg12AY.540.000095
S249L249LttGttA22AY.610.00021
S249L249LTtgCtg12B.10.000009
S249L249LttGttA12B.10.000009
S249L249delTTG---22B.1.10.000036
S249L249LttGttA22B.1.1.2140.000111
S249L249LttGttA22B.1.1.280.000622
S249L249FttGttT22B.1.1.330.000842
S249L249StTgtCg22B.1.1.5190.000079
S249L249delTTG---22B.1.20.000018
S249L249StTgtCg22B.1.36.290.001035
S249L249delTTG---22B.1.5250.000226
S249L249delTTG---22C.390.037736
S249L249MTtgAtg22D.20.00015
S249L249LttGttA22R.10.00018
S249L249delTTG---11A.2.50.000499
S249L249ITtGAtA11All0
S249L249del1TTG-NN11All0
S249L249ETTgGAg11All0
S249L249delTTG---11AY.1000.000046
S249L249delTTG---11AY.1010.00049
S249L249VTtgGtg11AY.1020.000027
S249L249StTgtCg11AY.1030.000006
S249L249WtTgtGg11AY.1030.000006
S249L249delTTG---11AY.1110.000183
S249L249LTtgCtg11AY.1110.000183
S249L249FttGttT11AY.1130.000142
S249L249FttGttT11AY.1140.000231
S249L249delTTG---11AY.1170.000085
S249L249StTgtCg11AY.1170.000085
S249L249FttGttT11AY.1180.000063
S249L249delTTG---11AY.1180.000063
S249L249FttGttT11AY.120.2.10.000498
S249L249StTgtCg11AY.160.00038
S249L249LttGttA11AY.200.000039
S249L249FttGttT11AY.200.000039
S249L249LttGttA11AY.230.00007
S249L249StTgtCg11AY.230.00007
S249L249StTgtCg11AY.250.000006
S249L249FttGttT11AY.260.000028
S249L249StTgtCg11AY.290.000016
S249L249LttGttA11AY.30.00001
S249L249del2tTGt--11AY.30.00001
S249L249StTgtCg11AY.330.000067
S249L249VTtgGtg11AY.40.000002
S249L249LttGttA11AY.4.20.000022
S249L249StTgtCg11AY.420.00004
S249L249VTtgGtg11AY.420.00004
S249L249WtTgtGg11AY.440.000006
S249L249LTtgCtg11AY.450.000122
S249L249StTgtCg11AY.470.000031
S249L249FttGttT11AY.470.000031
S249L249FttGttT11AY.50.000021
S249L249del2TTg--g11AY.50.000021
S249L249LTtgCtg11AY.5.40.000277
S249L249FttGttT11AY.590.00053
S249L249StTgtCg11AY.60.000041
S249L249FttGttT11AY.610.000105
S249L249delTTG---11AY.650.000533
S249L249LttGttA11AY.740.000116
S249L249LttGttA11AY.750.000056
S249L249StTgtCg11AY.850.000427
S249L249ETTgGAg11AY.850.000427
S249L249LttGttA11AY.9.10.000084
S249L249FttGttT11AY.9.20.000037
S249L249del2tTGt--11AY.9.20.000037
S249L249LttGttA11AY.9.20.000037
S249L249delTTG---11AY.950.000761
S249L249del1TTG-NN11AY.980.000079
S249L249XtTgtAg11B.10.000009
S249L249del2TTg--g11B.10.000009
S249L249delTTG---11B.1.1.10.000327
S249L249delTTG---11B.1.1.1590.004673
S249L249StTgtCg11B.1.1.1890.001513
S249L249StTgtCg11B.1.1.2140.000055
S249L249FttGttT11B.1.1.2160.00089
S249L249XtTgtAg11B.1.1.250.000569
S249L249FttGttT11B.1.1.3110.000358
S249L249WtTgtGg11B.1.1.3180.000302
S249L249FttGttT11B.1.1.3180.000302
S249L249LttGttA11B.1.1.3440.010753
S249L249delTTG---11B.1.1.3480.000796
S249L249StTgtCg11B.1.1.370.000193
S249L249delTTG---11B.1.1.3720.000689
S249L249StTgtCg11B.1.1.390.00051
S249L249WtTgtGg11B.1.1.5190.00004
S249L249delTTG---11B.1.1.5280.004808
S249L249MTtgAtg11B.1.1.70.000001
S249L249ITtGAtA11B.1.1.70.000001
S249L249LTtgCtg11B.1.1.990.02381
S249L249LttGttA11B.1.160.70.002079
S249L249WtTgtGg11B.1.1770.000013
S249L249LTtgCtg11B.1.177.60.000977
S249L249del2TTg--g11B.1.177.600.000218
S249L249delTTG---11B.1.177.690.001484
S249L249FttGttT11B.1.177.750.001041
S249L249delTTG---11B.1.177.760.002494
S249L249LttGttA11B.1.177.870.000728
S249L249StTgtCg11B.1.1870.033333
S249L249VTtgGtg11B.1.20.000009
S249L249FttGttT11B.1.230.006061
S249L249FttGttC11B.1.2320.000537
S249L249FttGttT11B.1.2360.002053
S249L249LttGttA11B.1.2580.000067
S249L249FttGttT11B.1.258.170.000104
S249L249FttGttC11B.1.3110.000275
S249L249StTgtCg11B.1.3110.000275
S249L249WtTgtGg11B.1.3320.003497
S249L249delTTG---11B.1.3510.00003
S249L249FttGttT11B.1.3620.001541
S249L249LTtgCtg11B.1.4270.00005
S249L249FttGttT11B.1.4270.00005
S249L249LttGttA11B.1.4290.000024
S249L249VTtgGtg11B.1.4290.000024
S249L249StTgtCg11B.1.4600.017857
S249L249VTtgGtg11B.1.5260.000024
S249L249delTTG---11B.1.5610.000397
S249L249LttGttA11B.1.5610.000397
S249L249LTtgCtg11B.1.5680.001111
S249L249StTgtCg11B.1.5860.010989
S249L249FttGttC11B.1.5960.000087
S249L249StTgtCg11B.1.5960.000087
S249L249VTtgGtg11B.1.6050.005952
S249L249VTtgGtg11B.1.617.20.000004
S249L249WtTgtGg11B.1.617.20.000004
S249L249delTTG---11B.1.6200.000946
S249L249StTgtCg11B.1.6230.000536
S249L249FttGttT11B.1.6370.000073
S249L249StTgtCg11B.400.000364
S249L249FttGttT11B.580.010204
S249L249StTgtCg11P.10.000016
S249L249delTTG---11P.1.10.000318
S249L249MTtgAtg11P.1.100.000269
S249L249MTtgAtg11P.1.120.000484
S249L249WtTgtGg11P.1.140.000048
S249L249LTtgCtg11Q.70.001111
S249L249WtTgtGg11R.10.00009

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.