CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 640

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/nsp12640R640RR5032RsyncgCcgT123811960.96607415358-15360
ORF1ab/nsp12640R640RR5032RsyncgCcgA1238330.026655915358-15360
ORF1ab/nsp12640R640RR5032RsyncgCcgG123890.0072697915358-15360
ORF1ab/nsp12640R640HR5032HnonsyncGccAc7171115358-15360
ORF1ab/nsp12640R640CR5032CnonsynCgcTgc4848115358-15360
ORF1ab/nsp12640R640SR5032SnonsynCgcAgc2727115358-15360
ORF1ab/nsp12640R640delR5032deldelCGC---1919115358-15360
ORF1ab/nsp12640R640PR5032PnonsyncGccCc1212115358-15360
ORF1ab/nsp12640R640LR5032LnonsyncGccTc88115358-15360
ORF1ab/nsp12640R640del2R5032del2delCGc--c430.7515358-15360
ORF1ab/nsp12640R640del2R5032del2delcGCc--410.2515358-15360
ORF1ab/nsp12640R640del1R5032del1delcGcc-c320.66666715358-15360
ORF1ab/nsp12640R640del1R5032del1delCgc-gc310.33333315358-15360
ORF1ab/nsp12640R640NR5032NnonsynCGcAAc11115358-15360
ORF1ab/nsp12640R640XR5032XnonsynCgCTgA11115358-15360

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/nsp12640R640RcgCcgT11961238All0.000229
ORF1ab/nsp12640R640RcgCcgA331238All0.000006
ORF1ab/nsp12640R640RcgCcgG91238All0.000002
ORF1ab/nsp12640R640RcgCcgT427429B.1.1.70.000382
ORF1ab/nsp12640R640RcgCcgA2429B.1.1.70.000002
ORF1ab/nsp12640R640RcgCcgT8485B.1.1600.00262
ORF1ab/nsp12640R640RcgCcgA185B.1.1600.000031
ORF1ab/nsp12640R640RcgCcgT7072B.1.617.20.000264
ORF1ab/nsp12640R640RcgCcgA272B.1.617.20.000008
ORF1ab/nsp12640R640HcGccAc7171All0.000014
ORF1ab/nsp12640R640RcgCcgT6264B.1.20.000546
ORF1ab/nsp12640R640RcgCcgA264B.1.20.000018
ORF1ab/nsp12640R640RcgCcgT5656AY.30.000557
ORF1ab/nsp12640R640CCgcTgc4848All0.000009
ORF1ab/nsp12640R640RcgCcgT4546AY.40.00007
ORF1ab/nsp12640R640RcgCcgA146AY.40.000002
ORF1ab/nsp12640R640RcgCcgT3939AY.250.000235
ORF1ab/nsp12640R640RcgCcgT3232AY.430.000142
ORF1ab/nsp12640R640RcgCcgT3131AY.440.000189
ORF1ab/nsp12640R640SCgcAgc2727All0.000005
ORF1ab/nsp12640R640RcgCcgT2323B.1.10.000417
ORF1ab/nsp12640R640delCGC---1919All0.000004
ORF1ab/nsp12640R640RcgCcgT1919AY.1190.000671
ORF1ab/nsp12640R640HcGccAc1616B.1.617.20.00006
ORF1ab/nsp12640R640RcgCcgT1616P.10.000252
ORF1ab/nsp12640R640RcgCcgT1515B.1.1.2140.000832
ORF1ab/nsp12640R640RcgCcgT1515B.1.1.3300.9375
ORF1ab/nsp12640R640CCgcTgc1515B.1.1.70.000013
ORF1ab/nsp12640R640RcgCcgT1014AY.1030.000062
ORF1ab/nsp12640R640RcgCcgA414AY.1030.000025
ORF1ab/nsp12640R640RcgCcgT1313AY.610.001362
ORF1ab/nsp12640R640PcGccCc1212All0.000002
ORF1ab/nsp12640R640RcgCcgT1112AY.1020.000292
ORF1ab/nsp12640R640RcgCcgA112AY.1020.000027
ORF1ab/nsp12640R640RcgCcgA612B.10.000055
ORF1ab/nsp12640R640RcgCcgT512B.10.000046
ORF1ab/nsp12640R640RcgCcgG112B.10.000009
ORF1ab/nsp12640R640RcgCcgT1111AY.420.000443
ORF1ab/nsp12640R640RcgCcgA611P.1.140.000287
ORF1ab/nsp12640R640RcgCcgT511P.1.140.000239
ORF1ab/nsp12640R640SCgcAgc99B.10.000082
ORF1ab/nsp12640R640delCGC---99B.1.1.70.000008
ORF1ab/nsp12640R640RcgCcgT99B.1.2430.000626
ORF1ab/nsp12640R640RcgCcgT99B.1.258.30.015075
ORF1ab/nsp12640R640RcgCcgT99B.1.3510.000268
ORF1ab/nsp12640R640LcGccTc88All0.000002
ORF1ab/nsp12640R640RcgCcgT88AY.1210.001083
ORF1ab/nsp12640R640RcgCcgT88AY.290.000126
ORF1ab/nsp12640R640RcgCcgT88AY.690.001493
ORF1ab/nsp12640R640RcgCcgT88B.1.1770.000105
ORF1ab/nsp12640R640RcgCcgT88B.1.177.600.001747
ORF1ab/nsp12640R640HcGccAc77AY.430.000031
ORF1ab/nsp12640R640RcgCcgT77B.1.177.210.000535
ORF1ab/nsp12640R640RcgCcgG77B.1.2580.000466
ORF1ab/nsp12640R640RcgCcgT66AY.120.2.10.00299
ORF1ab/nsp12640R640HcGccAc66B.1.1.70.000005
ORF1ab/nsp12640R640RcgCcgT55AY.130.000805
ORF1ab/nsp12640R640RcgCcgT55AY.200.000194
ORF1ab/nsp12640R640RcgCcgT55AY.4.20.000108
ORF1ab/nsp12640R640HcGccAc55B.1.20.000044
ORF1ab/nsp12640R640RcgCcgT55B.1.6210.000443
ORF1ab/nsp12640R640del2CGc--c34All0.000001
ORF1ab/nsp12640R640del2cGCc--14All0
ORF1ab/nsp12640R640CCgcTgc44AY.40.000006
ORF1ab/nsp12640R640HcGccAc44AY.40.000006
ORF1ab/nsp12640R640RcgCcgT44AY.50.000083
ORF1ab/nsp12640R640RcgCcgT44B.1.5260.000094
ORF1ab/nsp12640R640del1cGcc-c23All0
ORF1ab/nsp12640R640del1Cgc-gc13All0
ORF1ab/nsp12640R640RcgCcgT33AY.1170.000254
ORF1ab/nsp12640R640RcgCcgT33AY.140.000264
ORF1ab/nsp12640R640RcgCcgT23AY.260.000057
ORF1ab/nsp12640R640RcgCcgA13AY.260.000028
ORF1ab/nsp12640R640RcgCcgT33AY.330.0002
ORF1ab/nsp12640R640SCgcAgc33AY.430.000013
ORF1ab/nsp12640R640CCgcTgc33AY.46.60.000217
ORF1ab/nsp12640R640RcgCcgT33AY.470.000093
ORF1ab/nsp12640R640HcGccAc33AY.90.000203
ORF1ab/nsp12640R640RcgCcgT33AY.930.000819
ORF1ab/nsp12640R640PcGccCc33B.10.000027
ORF1ab/nsp12640R640CCgcTgc33B.1.10.000054
ORF1ab/nsp12640R640RcgCcgT33B.1.1.2940.003797
ORF1ab/nsp12640R640RcgCcgT33B.1.429.10.036145
ORF1ab/nsp12640R640RcgCcgT33B.1.5880.00273
ORF1ab/nsp12640R640PcGccCc33B.1.617.20.000011
ORF1ab/nsp12640R640RcgCcgT33B.60.00273
ORF1ab/nsp12640R640RcgCcgT33C.370.000348
ORF1ab/nsp12640R640CCgcTgc33D.20.000225
ORF1ab/nsp12640R640CCgcTgc22AY.1030.000012
ORF1ab/nsp12640R640RcgCcgT22AY.1140.000462
ORF1ab/nsp12640R640RcgCcgT22AY.1200.000074
ORF1ab/nsp12640R640HcGccAc22AY.200.000078
ORF1ab/nsp12640R640RcgCcgT22AY.230.000139
ORF1ab/nsp12640R640RcgCcgT22AY.390.000049
ORF1ab/nsp12640R640RcgCcgT22AY.39.10.000079
ORF1ab/nsp12640R640delCGC---22AY.4.50.000215
ORF1ab/nsp12640R640CCgcTgc22AY.440.000012
ORF1ab/nsp12640R640HcGccAc22AY.440.000012
ORF1ab/nsp12640R640RcgCcgT22AY.540.000191
ORF1ab/nsp12640R640RcgCcgT22AY.550.001835
ORF1ab/nsp12640R640RcgCcgA22AY.590.001059
ORF1ab/nsp12640R640RcgCcgT22AY.600.001876
ORF1ab/nsp12640R640RcgCcgA12AY.7.10.000113
ORF1ab/nsp12640R640RcgCcgT12AY.7.10.000113
ORF1ab/nsp12640R640RcgCcgT22AY.750.000112
ORF1ab/nsp12640R640RcgCcgT22AY.9.20.000073
ORF1ab/nsp12640R640RcgCcgT22AY.99.20.000184
ORF1ab/nsp12640R640CCgcTgc22B.10.000018
ORF1ab/nsp12640R640HcGccAc22B.1.1.1700.002494
ORF1ab/nsp12640R640PcGccCc22B.1.1.70.000002
ORF1ab/nsp12640R640LcGccTc22B.1.1.70.000002
ORF1ab/nsp12640R640del2CGc--c12B.1.1.70.000001
ORF1ab/nsp12640R640del2cGCc--12B.1.1.70.000001
ORF1ab/nsp12640R640HcGccAc22B.1.1770.000026
ORF1ab/nsp12640R640LcGccTc22B.1.20.000018
ORF1ab/nsp12640R640del1Cgc-gc12B.1.20.000009
ORF1ab/nsp12640R640del1cGcc-c12B.1.20.000009
ORF1ab/nsp12640R640HcGccAc22B.1.258.210.015504
ORF1ab/nsp12640R640PcGccCc22B.1.3510.000059
ORF1ab/nsp12640R640RcgCcgT22B.1.5600.009259
ORF1ab/nsp12640R640HcGccAc22B.1.5650.001621
ORF1ab/nsp12640R640SCgcAgc22B.60.00182
ORF1ab/nsp12640R640RcgCcgT22D.20.00015
ORF1ab/nsp12640R640PcGccCc110.055556
ORF1ab/nsp12640R640SCgcAgc11A0.000387
ORF1ab/nsp12640R640CCgcTgc11A.10.000282
ORF1ab/nsp12640R640HcGccAc11A.20.000662
ORF1ab/nsp12640R640RcgCcgT11A.2.5.20.001572
ORF1ab/nsp12640R640RcgCcgT11A.210.00277
ORF1ab/nsp12640R640XCgCTgA11All0
ORF1ab/nsp12640R640NCGcAAc11All0
ORF1ab/nsp12640R640RcgCcgG11AT.10.005128
ORF1ab/nsp12640R640RcgCcgT11AY.10.000396
ORF1ab/nsp12640R640HcGccAc11AY.1030.000006
ORF1ab/nsp12640R640NCGcAAc11AY.1030.000006
ORF1ab/nsp12640R640RcgCcgT11AY.1130.000142
ORF1ab/nsp12640R640RcgCcgT11AY.1180.000063
ORF1ab/nsp12640R640HcGccAc11AY.1200.000037
ORF1ab/nsp12640R640CCgcTgc11AY.250.000006
ORF1ab/nsp12640R640HcGccAc11AY.250.000006
ORF1ab/nsp12640R640HcGccAc11AY.260.000028
ORF1ab/nsp12640R640CCgcTgc11AY.260.000028
ORF1ab/nsp12640R640CCgcTgc11AY.290.000016
ORF1ab/nsp12640R640del2CGc--c11AY.30.00001
ORF1ab/nsp12640R640RcgCcgT11AY.340.000097
ORF1ab/nsp12640R640HcGccAc11AY.390.000025
ORF1ab/nsp12640R640CCgcTgc11AY.4.20.000022
ORF1ab/nsp12640R640HcGccAc11AY.420.00004
ORF1ab/nsp12640R640LcGccTc11AY.430.000004
ORF1ab/nsp12640R640HcGccAc11AY.450.000122
ORF1ab/nsp12640R640RcgCcgT11AY.46.40.000165
ORF1ab/nsp12640R640RcgCcgT11AY.46.60.000072
ORF1ab/nsp12640R640SCgcAgc11AY.470.000031
ORF1ab/nsp12640R640RcgCcgT11AY.480.000465
ORF1ab/nsp12640R640RcgCcgT11AY.490.003195
ORF1ab/nsp12640R640CCgcTgc11AY.50.000021
ORF1ab/nsp12640R640SCgcAgc11AY.5.40.000277
ORF1ab/nsp12640R640SCgcAgc11AY.520.000814
ORF1ab/nsp12640R640RcgCcgT11AY.60.000041
ORF1ab/nsp12640R640HcGccAc11AY.690.000187
ORF1ab/nsp12640R640RcgCcgT11AY.710.000475
ORF1ab/nsp12640R640RcgCcgT11AY.740.000116
ORF1ab/nsp12640R640HcGccAc11AY.750.000056
ORF1ab/nsp12640R640RcgCcgT11AY.75.10.00018
ORF1ab/nsp12640R640RcgCcgT11AY.790.001211
ORF1ab/nsp12640R640RcgCcgT11AY.840.000437
ORF1ab/nsp12640R640RcgCcgT11AY.90.000068
ORF1ab/nsp12640R640RcgCcgT11AY.910.00073
ORF1ab/nsp12640R640SCgcAgc11B0.000128
ORF1ab/nsp12640R640HcGccAc11B.10.000009
ORF1ab/nsp12640R640LcGccTc11B.10.000009
ORF1ab/nsp12640R640del1cGcc-c11B.10.000009
ORF1ab/nsp12640R640SCgcAgc11B.1.10.000018
ORF1ab/nsp12640R640RcgCcgT11B.1.1.10.000327
ORF1ab/nsp12640R640CCgcTgc11B.1.1.1230.017857
ORF1ab/nsp12640R640HcGccAc11B.1.1.1410.002012
ORF1ab/nsp12640R640RcgCcgT11B.1.1.2160.00089
ORF1ab/nsp12640R640HcGccAc11B.1.1.250.000569
ORF1ab/nsp12640R640RcgCcgA11B.1.1.2860.002899
ORF1ab/nsp12640R640RcgCcgT11B.1.1.3010.001179
ORF1ab/nsp12640R640RcgCcgT11B.1.1.330.000421
ORF1ab/nsp12640R640CCgcTgc11B.1.1.3330.001076
ORF1ab/nsp12640R640RcgCcgT11B.1.1.370.000193
ORF1ab/nsp12640R640SCgcAgc11B.1.1.4170.002703
ORF1ab/nsp12640R640SCgcAgc11B.1.1.70.000001
ORF1ab/nsp12640R640delCGC---11B.1.1.700.000341
ORF1ab/nsp12640R640HcGccAc11B.1.1460.004237
ORF1ab/nsp12640R640delCGC---11B.1.160.230.004831
ORF1ab/nsp12640R640delCGC---11B.1.1770.000013
ORF1ab/nsp12640R640LcGccTc11B.1.1770.000013
ORF1ab/nsp12640R640delCGC---11B.1.177.180.00116
ORF1ab/nsp12640R640RcgCcgT11B.1.177.450.000381
ORF1ab/nsp12640R640delCGC---11B.1.177.540.000606
ORF1ab/nsp12640R640RcgCcgA11B.1.177.730.000566
ORF1ab/nsp12640R640RcgCcgA11B.1.177.770.000726
ORF1ab/nsp12640R640RcgCcgT11B.1.177.810.000189
ORF1ab/nsp12640R640SCgcAgc11B.1.20.000009
ORF1ab/nsp12640R640CCgcTgc11B.1.20.000009
ORF1ab/nsp12640R640SCgcAgc11B.1.3010.005917
ORF1ab/nsp12640R640CCgcTgc11B.1.3110.000275
ORF1ab/nsp12640R640LcGccTc11B.1.36.100.004785
ORF1ab/nsp12640R640RcgCcgT11B.1.36.160.001425
ORF1ab/nsp12640R640delCGC---11B.1.36.290.000517
ORF1ab/nsp12640R640HcGccAc11B.1.36.290.000517
ORF1ab/nsp12640R640CCgcTgc11B.1.36.390.002217
ORF1ab/nsp12640R640RcgCcgT11B.1.370.014706
ORF1ab/nsp12640R640RcgCcgT11B.1.4080.00369
ORF1ab/nsp12640R640RcgCcgT11B.1.4160.001269
ORF1ab/nsp12640R640RcgCcgT11B.1.4290.000024
ORF1ab/nsp12640R640CCgcTgc11B.1.4290.000024
ORF1ab/nsp12640R640HcGccAc11B.1.466.20.000391
ORF1ab/nsp12640R640delCGC---11B.1.4970.000315
ORF1ab/nsp12640R640RcgCcgT11B.1.5250.000113
ORF1ab/nsp12640R640del2CGc--c11B.1.5260.000024
ORF1ab/nsp12640R640CCgcTgc11B.1.5950.000261
ORF1ab/nsp12640R640HcGccAc11B.1.5950.000261
ORF1ab/nsp12640R640CCgcTgc11B.1.5960.000087
ORF1ab/nsp12640R640PcGccCc11B.1.6000.005848
ORF1ab/nsp12640R640RcgCcgT11B.1.6090.000479
ORF1ab/nsp12640R640RcgCcgT11B.1.6160.02439
ORF1ab/nsp12640R640RcgCcgT11B.1.617.10.000129
ORF1ab/nsp12640R640XCgCTgA11B.1.617.20.000004
ORF1ab/nsp12640R640delCGC---11B.1.617.20.000004
ORF1ab/nsp12640R640RcgCcgT11B.1.6180.004032
ORF1ab/nsp12640R640RcgCcgT11B.1.6200.000946
ORF1ab/nsp12640R640SCgcAgc11B.1.6230.000536
ORF1ab/nsp12640R640RcgCcgT11B.1.9.50.005682
ORF1ab/nsp12640R640RcgCcgT11B.550.00295
ORF1ab/nsp12640R640SCgcAgc11B.6.60.000889
ORF1ab/nsp12640R640RcgCcgA11C.350.000774
ORF1ab/nsp12640R640HcGccAc11P.1.140.000048
ORF1ab/nsp12640R640SCgcAgc11Q.80.000165
ORF1ab/nsp12640R640RcgCcgT11Q.80.000165
ORF1ab/nsp12640R640RcgCcgT11R.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.