CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp13 : CodonNum = 63

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/nsp1363L63LL5387LsynctTctG229212500.54537516423-16425
ORF1ab/nsp1363L63LL5387LsynctTctA22929440.41186716423-16425
ORF1ab/nsp1363L63LL5387LsynctTctC2292980.042757416423-16425
ORF1ab/nsp1363L63delL5387deldelCTT---5959116423-16425
ORF1ab/nsp1363L63PL5387PnonsyncTtcCt26240.92307716423-16425
ORF1ab/nsp1363L63IL5387InonsynCttAtt26240.92307716423-16425
ORF1ab/nsp1363L63PL5387PnonsyncTTcCC2610.038461516423-16425
ORF1ab/nsp1363L63IL5387InonsynCtTAtC2610.038461516423-16425
ORF1ab/nsp1363L63PL5387PnonsyncTTcCA2610.038461516423-16425
ORF1ab/nsp1363L63IL5387InonsynCtTAtA2610.038461516423-16425
ORF1ab/nsp1363L63FL5387FnonsynCttTtt22190.86363616423-16425
ORF1ab/nsp1363L63FL5387FnonsynCtTTtC2230.13636416423-16425
ORF1ab/nsp1363L63del1L5387del1delcTtc-t1180.72727316423-16425
ORF1ab/nsp1363L63del1L5387del1delCtt-tt1120.18181816423-16425
ORF1ab/nsp1363L63del1L5387del1delCtT-tN1110.090909116423-16425
ORF1ab/nsp1363L63HL5387HnonsyncTtcAt850.62516423-16425
ORF1ab/nsp1363L63HL5387HnonsyncTTcAC830.37516423-16425
ORF1ab/nsp1363L63VL5387VnonsynCttGtt77116423-16425
ORF1ab/nsp1363L63RL5387RnonsyncTtcGt44116423-16425
ORF1ab/nsp1363L63TL5387TnonsynCTtACt420.516423-16425
ORF1ab/nsp1363L63YL5387YnonsynCTtTAt420.516423-16425
ORF1ab/nsp1363L63YL5387YnonsynCTTTAC420.516423-16425
ORF1ab/nsp1363L63TL5387TnonsynCTTACA420.516423-16425
ORF1ab/nsp1363L63del2L5387del2delCTt--t210.516423-16425
ORF1ab/nsp1363L63del2L5387del2delcTTc--210.516423-16425
ORF1ab/nsp1363L63NL5387NnonsynCTTAAC11116423-16425

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/nsp1363L63LctTctG12502292All0.000239
ORF1ab/nsp1363L63LctTctA9442292All0.000181
ORF1ab/nsp1363L63LctTctC982292All0.000019
ORF1ab/nsp1363L63LctTctA885885AY.4.20.019194
ORF1ab/nsp1363L63LctTctG707707B.1.5760.640979
ORF1ab/nsp1363L63LctTctG415415B.1.5740.892473
ORF1ab/nsp1363L63LctTctG5667B.10.000513
ORF1ab/nsp1363L63LctTctA867B.10.000073
ORF1ab/nsp1363L63LctTctC367B.10.000027
ORF1ab/nsp1363L63delCTT---5959All0.000011
ORF1ab/nsp1363L63LctTctG5555B.1.3630.714286
ORF1ab/nsp1363L63LctTctA3132AY.40.000048
ORF1ab/nsp1363L63LctTctC132AY.40.000002
ORF1ab/nsp1363L63delCTT---3131B.1.1.70.000028
ORF1ab/nsp1363L63ICttAtt2426All0.000005
ORF1ab/nsp1363L63PcTtcCt2426All0.000005
ORF1ab/nsp1363L63ICtTAtC126All0
ORF1ab/nsp1363L63ICtTAtA126All0
ORF1ab/nsp1363L63PcTTcCA126All0
ORF1ab/nsp1363L63PcTTcCC126All0
ORF1ab/nsp1363L63FCttTtt1922All0.000004
ORF1ab/nsp1363L63FCtTTtC322All0.000001
ORF1ab/nsp1363L63LctTctC1920B.1.1.70.000017
ORF1ab/nsp1363L63LctTctG120B.1.1.70.000001
ORF1ab/nsp1363L63LctTctA1920B.1.617.20.000072
ORF1ab/nsp1363L63LctTctC120B.1.617.20.000004
ORF1ab/nsp1363L63LctTctC1717B.1.1.5190.000675
ORF1ab/nsp1363L63del1cTtc-t811All0.000002
ORF1ab/nsp1363L63del1Ctt-tt211All0
ORF1ab/nsp1363L63del1CtT-tN111All0
ORF1ab/nsp1363L63LctTctC1010AY.120.10.00321
ORF1ab/nsp1363L63HcTtcAt58All0.000001
ORF1ab/nsp1363L63HcTTcAC38All0.000001
ORF1ab/nsp1363L63LctTctC48B.1.20.000035
ORF1ab/nsp1363L63LctTctG48B.1.20.000035
ORF1ab/nsp1363L63VCttGtt77All0.000001
ORF1ab/nsp1363L63HcTtcAt460.222222
ORF1ab/nsp1363L63HcTTcAC260.111111
ORF1ab/nsp1363L63PcTtcCt66B.1.1.70.000005
ORF1ab/nsp1363L63FCttTtt240.111111
ORF1ab/nsp1363L63YCTtTAt240.111111
ORF1ab/nsp1363L63YCTTTAC240.111111
ORF1ab/nsp1363L63FCtTTtC240.111111
ORF1ab/nsp1363L63RcTtcGt44All0.000001
ORF1ab/nsp1363L63TCTtACt24All0
ORF1ab/nsp1363L63YCTTTAC24All0
ORF1ab/nsp1363L63TCTTACA24All0
ORF1ab/nsp1363L63YCTtTAt24All0
ORF1ab/nsp1363L63LctTctC44B.1.6200.003784
ORF1ab/nsp1363L63ICttAtt33AY.440.000018
ORF1ab/nsp1363L63LctTctC33AY.50.000062
ORF1ab/nsp1363L63FCttTtt33B.10.000027
ORF1ab/nsp1363L63delCTT---33B.1.10.000054
ORF1ab/nsp1363L63VCttGtt33B.1.1.5190.000119
ORF1ab/nsp1363L63FCttTtt33B.1.1.70.000003
ORF1ab/nsp1363L63LctTctC33B.1.1770.00004
ORF1ab/nsp1363L63delCTT---33B.1.1770.00004
ORF1ab/nsp1363L63LctTctG33B.1.2580.0002
ORF1ab/nsp1363L63LctTctG33B.1.5960.000261
ORF1ab/nsp1363L63delCTT---33B.1.617.20.000011
ORF1ab/nsp1363L63LctTctC33P.1.150.000697
ORF1ab/nsp1363L63LctTctC220.111111
ORF1ab/nsp1363L63delCTT---220.111111
ORF1ab/nsp1363L63RcTtcGt220.111111
ORF1ab/nsp1363L63del2CTt--t12All0
ORF1ab/nsp1363L63del2cTTc--12All0
ORF1ab/nsp1363L63LctTctC22AY.430.000009
ORF1ab/nsp1363L63delCTT---22AY.430.000009
ORF1ab/nsp1363L63ICttAtt22AY.680.000547
ORF1ab/nsp1363L63TCTtACt12AY.990.001049
ORF1ab/nsp1363L63ICttAtt12AY.990.001049
ORF1ab/nsp1363L63PcTtcCt12AY.990.001049
ORF1ab/nsp1363L63PcTTcCA12AY.990.001049
ORF1ab/nsp1363L63ICtTAtA12AY.990.001049
ORF1ab/nsp1363L63TCTTACA12AY.990.001049
ORF1ab/nsp1363L63ICttAtt22B.10.000018
ORF1ab/nsp1363L63del1cTtc-t22B.10.000018
ORF1ab/nsp1363L63FCttTtt22B.1.10.000036
ORF1ab/nsp1363L63PcTtcCt22B.1.10.000036
ORF1ab/nsp1363L63ICttAtt22B.1.1.1410.004024
ORF1ab/nsp1363L63RcTtcGt22B.1.1.70.000002
ORF1ab/nsp1363L63ICttAtt22B.1.1.70.000002
ORF1ab/nsp1363L63PcTtcCt22B.1.20.000018
ORF1ab/nsp1363L63LctTctC22B.1.2060.001631
ORF1ab/nsp1363L63LctTctC12B.1.2400.000216
ORF1ab/nsp1363L63LctTctG12B.1.2400.000216
ORF1ab/nsp1363L63LctTctC22B.1.360.000292
ORF1ab/nsp1363L63ICttAtt22B.1.4290.000047
ORF1ab/nsp1363L63LctTctC22B.1.466.10.014388
ORF1ab/nsp1363L63FCttTtt22B.1.617.20.000008
ORF1ab/nsp1363L63del1cTtc-t22P.1.140.000096
ORF1ab/nsp1363L63LctTctC22Q.10.000253
ORF1ab/nsp1363L63ICttAtt110.055556
ORF1ab/nsp1363L63TCTtACt110.055556
ORF1ab/nsp1363L63VCttGtt110.055556
ORF1ab/nsp1363L63PcTtcCt110.055556
ORF1ab/nsp1363L63PcTtcCt11AD.20.000219
ORF1ab/nsp1363L63NCTTAAC11All0
ORF1ab/nsp1363L63del1Ctt-tt11AU.10.001266
ORF1ab/nsp1363L63HcTTcAC11AY.1030.000006
ORF1ab/nsp1363L63FCtTTtC11AY.1030.000006
ORF1ab/nsp1363L63ICttAtt11AY.1030.000006
ORF1ab/nsp1363L63LctTctC11AY.1050.000643
ORF1ab/nsp1363L63LctTctC11AY.1070.000466
ORF1ab/nsp1363L63delCTT---11AY.1110.000183
ORF1ab/nsp1363L63del2CTt--t11AY.1130.000142
ORF1ab/nsp1363L63PcTtcCt11AY.116.10.000311
ORF1ab/nsp1363L63LctTctC11AY.1190.000035
ORF1ab/nsp1363L63PcTtcCt11AY.250.000006
ORF1ab/nsp1363L63LctTctC11AY.250.000006
ORF1ab/nsp1363L63del1Ctt-tt11AY.250.000006
ORF1ab/nsp1363L63LctTctC11AY.290.000016
ORF1ab/nsp1363L63delCTT---11AY.330.000067
ORF1ab/nsp1363L63ICttAtt11AY.40.000002
ORF1ab/nsp1363L63PcTtcCt11AY.40.000002
ORF1ab/nsp1363L63delCTT---11AY.40.000002
ORF1ab/nsp1363L63delCTT---11AY.4.50.000107
ORF1ab/nsp1363L63ICttAtt11AY.4.50.000107
ORF1ab/nsp1363L63FCttTtt11AY.430.000004
ORF1ab/nsp1363L63del2cTTc--11AY.440.000006
ORF1ab/nsp1363L63PcTTcCC11AY.440.000006
ORF1ab/nsp1363L63LctTctC11AY.440.000006
ORF1ab/nsp1363L63LctTctC11AY.470.000031
ORF1ab/nsp1363L63ICtTAtC11AY.480.000465
ORF1ab/nsp1363L63LctTctC11AY.590.00053
ORF1ab/nsp1363L63NCTTAAC11AY.670.000464
ORF1ab/nsp1363L63LctTctC11AY.75.10.00018
ORF1ab/nsp1363L63FCttTtt11AY.980.000079
ORF1ab/nsp1363L63LctTctA11AY.990.001049
ORF1ab/nsp1363L63HcTtcAt11B.1.10.000018
ORF1ab/nsp1363L63LctTctG11B.1.10.000018
ORF1ab/nsp1363L63PcTtcCt11B.1.1.10.000327
ORF1ab/nsp1363L63VCttGtt11B.1.1.2220.000204
ORF1ab/nsp1363L63LctTctC11B.1.1.270.00565
ORF1ab/nsp1363L63TCTTACA11B.1.1.3060.000438
ORF1ab/nsp1363L63PcTtcCt11B.1.1.3650.005587
ORF1ab/nsp1363L63LctTctC11B.1.1.370.000193
ORF1ab/nsp1363L63PcTtcCt11B.1.1.410.006329
ORF1ab/nsp1363L63ICttAtt11B.1.1.50.008333
ORF1ab/nsp1363L63del1CtT-tN11B.1.1.70.000001
ORF1ab/nsp1363L63VCttGtt11B.1.1.70.000001
ORF1ab/nsp1363L63delCTT---11B.1.1.700.000341
ORF1ab/nsp1363L63delCTT---11B.1.1600.000031
ORF1ab/nsp1363L63ICttAtt11B.1.1770.000013
ORF1ab/nsp1363L63FCttTtt11B.1.1770.000013
ORF1ab/nsp1363L63delCTT---11B.1.177.40.000211
ORF1ab/nsp1363L63delCTT---11B.1.177.620.001192
ORF1ab/nsp1363L63delCTT---11B.1.177.680.015152
ORF1ab/nsp1363L63delCTT---11B.1.177.70.000165
ORF1ab/nsp1363L63delCTT---11B.1.177.730.000566
ORF1ab/nsp1363L63delCTT---11B.1.177.830.001481
ORF1ab/nsp1363L63del1cTtc-t11B.1.20.000009
ORF1ab/nsp1363L63ICttAtt11B.1.20.000009
ORF1ab/nsp1363L63FCttTtt11B.1.20.000009
ORF1ab/nsp1363L63ICttAtt11B.1.2210.000071
ORF1ab/nsp1363L63FCttTtt11B.1.2340.000132
ORF1ab/nsp1363L63FCttTtt11B.1.2430.00007
ORF1ab/nsp1363L63delCTT---11B.1.2580.000067
ORF1ab/nsp1363L63LctTctC11B.1.2680.010417
ORF1ab/nsp1363L63LctTctG11B.1.3490.000715
ORF1ab/nsp1363L63del1cTtc-t11B.1.4040.001302
ORF1ab/nsp1363L63delCTT---11B.1.416.10.001563
ORF1ab/nsp1363L63VCttGtt11B.1.4290.000024
ORF1ab/nsp1363L63FCttTtt11B.1.4800.002488
ORF1ab/nsp1363L63LctTctG11B.1.4990.00105
ORF1ab/nsp1363L63LctTctG11B.1.5110.034483
ORF1ab/nsp1363L63PcTtcCt11B.1.5680.001111
ORF1ab/nsp1363L63del1cTtc-t11B.1.617.10.000129
ORF1ab/nsp1363L63ICttAtt11B.1.617.20.000004
ORF1ab/nsp1363L63PcTtcCt11B.1.617.20.000004
ORF1ab/nsp1363L63del1cTtc-t11B.1.617.20.000004
ORF1ab/nsp1363L63delCTT---11B.1.617.30.002985
ORF1ab/nsp1363L63PcTtcCt11B.1.6210.000089
ORF1ab/nsp1363L63LctTctC11B.1.6210.000089
ORF1ab/nsp1363L63PcTtcCt11B.400.000364
ORF1ab/nsp1363L63ICttAtt11B.60.00091
ORF1ab/nsp1363L63LctTctC11B.6.60.000889
ORF1ab/nsp1363L63LctTctC11C.370.000116
ORF1ab/nsp1363L63PcTtcCt11D.20.000075
ORF1ab/nsp1363L63LctTctG11D.20.000075
ORF1ab/nsp1363L63LctTctC11P.10.000016
ORF1ab/nsp1363L63LctTctC11P.20.000187

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.