CoV-GLUEGenomeCountriesLineagesMutationsInsertionsDeletionsUpdated:

CoV-GLUE | Mutations | Mutation

CoV-GLUE Mutation: ORF = ORF1ab/nsp12 : CodonNum = 253

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/nsp12253A253AA4645AsyngcAgcG5284570.8655314197-14199
ORF1ab/nsp12253A253AA4645AsyngcAgcT528570.10795514197-14199
ORF1ab/nsp12253A253AA4645AsyngcAgcC528140.026515214197-14199
ORF1ab/nsp12253A253SA4645SnonsynGcaTca156156114197-14199
ORF1ab/nsp12253A253VA4645VnonsyngCagTa82770.93902414197-14199
ORF1ab/nsp12253A253VA4645VnonsyngCAgTT8240.048780514197-14199
ORF1ab/nsp12253A253VA4645VnonsyngCAgTG8210.012195114197-14199
ORF1ab/nsp12253A253TA4645TnonsynGcaAca24230.95833314197-14199
ORF1ab/nsp12253A253TA4645TnonsynGcAAcG2410.041666714197-14199
ORF1ab/nsp12253A253delA4645deldelGCA---1616114197-14199
ORF1ab/nsp12253A253PA4645PnonsynGcaCca760.85714314197-14199
ORF1ab/nsp12253A253PA4645PnonsynGcACcG710.14285714197-14199
ORF1ab/nsp12253A253EA4645EnonsyngCagAa540.814197-14199
ORF1ab/nsp12253A253EA4645EnonsyngCAgAG510.214197-14199
ORF1ab/nsp12253A253del1A4645del1delgcAgc-420.514197-14199
ORF1ab/nsp12253A253del1A4645del1delgCag-a410.2514197-14199
ORF1ab/nsp12253A253del1A4645del1delGca-ca410.2514197-14199
ORF1ab/nsp12253A253GA4645GnonsyngCagGa33114197-14199
ORF1ab/nsp12253A253LA4645LnonsynGCaCTa210.514197-14199
ORF1ab/nsp12253A253QA4645QnonsynGCACAG210.514197-14199
ORF1ab/nsp12253A253QA4645QnonsynGCaCAa210.514197-14199
ORF1ab/nsp12253A253LA4645LnonsynGCACTG210.514197-14199

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/nsp12253A253AgcAgcG457528All0.000087
ORF1ab/nsp12253A253AgcAgcT57528All0.000011
ORF1ab/nsp12253A253AgcAgcC14528All0.000003
ORF1ab/nsp12253A253SGcaTca156156All0.00003
ORF1ab/nsp12253A253AgcAgcG133144B.1.1.70.000119
ORF1ab/nsp12253A253AgcAgcT7144B.1.1.70.000006
ORF1ab/nsp12253A253AgcAgcC4144B.1.1.70.000004
ORF1ab/nsp12253A253AgcAgcG127130B.1.20.001118
ORF1ab/nsp12253A253AgcAgcC2130B.1.20.000018
ORF1ab/nsp12253A253AgcAgcT1130B.1.20.000009
ORF1ab/nsp12253A253VgCagTa7782All0.000015
ORF1ab/nsp12253A253VgCAgTT482All0.000001
ORF1ab/nsp12253A253VgCAgTG182All0
ORF1ab/nsp12253A253SGcaTca6060D.20.004502
ORF1ab/nsp12253A253AgcAgcG4848B.1.1.4320.060759
ORF1ab/nsp12253A253AgcAgcG2531B.10.000229
ORF1ab/nsp12253A253AgcAgcT531B.10.000046
ORF1ab/nsp12253A253AgcAgcC131B.10.000009
ORF1ab/nsp12253A253SGcaTca2626AY.250.000156
ORF1ab/nsp12253A253TGcaAca2324All0.000004
ORF1ab/nsp12253A253TGcAAcG124All0
ORF1ab/nsp12253A253AgcAgcG1323AY.30.000129
ORF1ab/nsp12253A253AgcAgcT1023AY.30.000099
ORF1ab/nsp12253A253delGCA---1616All0.000003
ORF1ab/nsp12253A253VgCagTa1616AY.40.000025
ORF1ab/nsp12253A253AgcAgcG1515B.1.360.002189
ORF1ab/nsp12253A253AgcAgcG1414B.1.5820.006869
ORF1ab/nsp12253A253AgcAgcT913AY.40.000014
ORF1ab/nsp12253A253AgcAgcG413AY.40.000006
ORF1ab/nsp12253A253AgcAgcG1011B.1.617.20.000038
ORF1ab/nsp12253A253AgcAgcT111B.1.617.20.000004
ORF1ab/nsp12253A253SGcaTca1010P.1.70.003193
ORF1ab/nsp12253A253SGcaTca99B.10.000082
ORF1ab/nsp12253A253VgCagTa88B.1.1.70.000007
ORF1ab/nsp12253A253PGcaCca67All0.000001
ORF1ab/nsp12253A253PGcACcG17All0
ORF1ab/nsp12253A253VgCagTa77B.10.000064
ORF1ab/nsp12253A253SGcaTca77B.1.10.000127
ORF1ab/nsp12253A253AgcAgcG77B.1.1770.000092
ORF1ab/nsp12253A253AgcAgcT77B.1.350.11
ORF1ab/nsp12253A253TGcaAca66AY.40.000009
ORF1ab/nsp12253A253AgcAgcG36AY.440.000018
ORF1ab/nsp12253A253AgcAgcC26AY.440.000012
ORF1ab/nsp12253A253AgcAgcT16AY.440.000006
ORF1ab/nsp12253A253delGCA---66B.1.1.70.000005
ORF1ab/nsp12253A253SGcaTca66B.1.1.70.000005
ORF1ab/nsp12253A253AgcAgcT36P.10.000047
ORF1ab/nsp12253A253AgcAgcG36P.10.000047
ORF1ab/nsp12253A253EgCagAa45All0.000001
ORF1ab/nsp12253A253EgCAgAG15All0
ORF1ab/nsp12253A253AgcAgcT35AY.250.000018
ORF1ab/nsp12253A253AgcAgcC25AY.250.000012
ORF1ab/nsp12253A253AgcAgcG55AY.300.001979
ORF1ab/nsp12253A253del1gcAgc-24All0
ORF1ab/nsp12253A253del1Gca-ca14All0
ORF1ab/nsp12253A253del1gCag-a14All0
ORF1ab/nsp12253A253SGcaTca44AY.40.000006
ORF1ab/nsp12253A253AgcAgcG44B.1.160.170.006803
ORF1ab/nsp12253A253VgCagTa44B.1.617.20.000015
ORF1ab/nsp12253A253VgCagTa44B.400.001457
ORF1ab/nsp12253A253VgCagTa33A0.001161
ORF1ab/nsp12253A253TGcaAca33A.10.000846
ORF1ab/nsp12253A253AgcAgcG33A.10.000846
ORF1ab/nsp12253A253VgCagTa33A.250.054545
ORF1ab/nsp12253A253GgCagGa33All0.000001
ORF1ab/nsp12253A253AgcAgcG33AY.1030.000019
ORF1ab/nsp12253A253VgCAgTT23AY.30.00002
ORF1ab/nsp12253A253VgCagTa13AY.30.00001
ORF1ab/nsp12253A253AgcAgcT33B.1.1.5190.000119
ORF1ab/nsp12253A253TGcaAca33B.1.1.70.000003
ORF1ab/nsp12253A253AgcAgcG33B.1.3370.01676
ORF1ab/nsp12253A253VgCagTa33B.1.5960.000261
ORF1ab/nsp12253A253TGcaAca33B.1.617.20.000011
ORF1ab/nsp12253A253PGcaCca120.055556
ORF1ab/nsp12253A253LGCACTG120.055556
ORF1ab/nsp12253A253VgCAgTG120.055556
ORF1ab/nsp12253A253LGCaCTa120.055556
ORF1ab/nsp12253A253EgCagAa120.055556
ORF1ab/nsp12253A253PGcACcG120.055556
ORF1ab/nsp12253A253QGCACAG120.055556
ORF1ab/nsp12253A253EgCAgAG120.055556
ORF1ab/nsp12253A253VgCagTa120.055556
ORF1ab/nsp12253A253QGCaCAa120.055556
ORF1ab/nsp12253A253SGcaTca22A.20.001324
ORF1ab/nsp12253A253QGCACAG12All0
ORF1ab/nsp12253A253LGCaCTa12All0
ORF1ab/nsp12253A253LGCACTG12All0
ORF1ab/nsp12253A253QGCaCAa12All0
ORF1ab/nsp12253A253AgcAgcG22AY.1000.000092
ORF1ab/nsp12253A253SGcaTca22AY.1020.000053
ORF1ab/nsp12253A253VgCagTa22AY.1190.000071
ORF1ab/nsp12253A253AgcAgcG12AY.1190.000035
ORF1ab/nsp12253A253AgcAgcT12AY.1190.000035
ORF1ab/nsp12253A253GgCagGa22AY.1200.000074
ORF1ab/nsp12253A253AgcAgcG22AY.230.000139
ORF1ab/nsp12253A253SGcaTca22AY.290.000032
ORF1ab/nsp12253A253SGcaTca22AY.420.00008
ORF1ab/nsp12253A253AgcAgcG22AY.450.000243
ORF1ab/nsp12253A253AgcAgcG22B.1.1600.000062
ORF1ab/nsp12253A253SGcaTca22B.1.1770.000026
ORF1ab/nsp12253A253VgCagTa22B.1.1770.000026
ORF1ab/nsp12253A253VgCagTa22B.1.20.000018
ORF1ab/nsp12253A253delGCA---22B.1.20.000018
ORF1ab/nsp12253A253AgcAgcT22B.1.2210.000142
ORF1ab/nsp12253A253SGcaTca22B.1.2340.000264
ORF1ab/nsp12253A253SGcaTca22B.1.4270.000101
ORF1ab/nsp12253A253AgcAgcG22B.1.4290.000047
ORF1ab/nsp12253A253VgCagTa22B.1.4290.000047
ORF1ab/nsp12253A253SGcaTca22B.1.617.20.000008
ORF1ab/nsp12253A253AgcAgcG110.055556
ORF1ab/nsp12253A253TGcaAca11A0.000387
ORF1ab/nsp12253A253AgcAgcG11AY.1020.000027
ORF1ab/nsp12253A253VgCagTa11AY.1020.000027
ORF1ab/nsp12253A253VgCagTa11AY.1030.000006
ORF1ab/nsp12253A253AgcAgcG11AY.1060.000335
ORF1ab/nsp12253A253TGcAAcG11AY.1190.000035
ORF1ab/nsp12253A253delGCA---11AY.1200.000037
ORF1ab/nsp12253A253AgcAgcG11AY.1200.000037
ORF1ab/nsp12253A253SGcaTca11AY.130.000161
ORF1ab/nsp12253A253EgCagAa11AY.130.000161
ORF1ab/nsp12253A253AgcAgcC11AY.140.000088
ORF1ab/nsp12253A253VgCagTa11AY.16.10.00047
ORF1ab/nsp12253A253VgCagTa11AY.230.00007
ORF1ab/nsp12253A253EgCagAa11AY.250.000006
ORF1ab/nsp12253A253VgCagTa11AY.250.000006
ORF1ab/nsp12253A253TGcaAca11AY.270.000065
ORF1ab/nsp12253A253TGcaAca11AY.30.00001
ORF1ab/nsp12253A253AgcAgcG11AY.380.000499
ORF1ab/nsp12253A253delGCA---11AY.390.000025
ORF1ab/nsp12253A253VgCAgTT11AY.390.000025
ORF1ab/nsp12253A253SGcaTca11AY.390.000025
ORF1ab/nsp12253A253AgcAgcG11AY.390.000025
ORF1ab/nsp12253A253AgcAgcG11AY.39.10.00004
ORF1ab/nsp12253A253delGCA---11AY.40.000002
ORF1ab/nsp12253A253PGcaCca11AY.40.000002
ORF1ab/nsp12253A253AgcAgcG11AY.430.000004
ORF1ab/nsp12253A253VgCagTa11AY.430.000004
ORF1ab/nsp12253A253SGcaTca11AY.440.000006
ORF1ab/nsp12253A253AgcAgcG11AY.46.40.000165
ORF1ab/nsp12253A253AgcAgcC11AY.470.000031
ORF1ab/nsp12253A253AgcAgcT11AY.590.00053
ORF1ab/nsp12253A253SGcaTca11AY.650.000533
ORF1ab/nsp12253A253delGCA---11AY.650.000533
ORF1ab/nsp12253A253AgcAgcT11AY.740.000116
ORF1ab/nsp12253A253delGCA---11AY.80.000606
ORF1ab/nsp12253A253AgcAgcC11AY.850.000427
ORF1ab/nsp12253A253VgCagTa11AY.9.10.000084
ORF1ab/nsp12253A253AgcAgcG11AY.9.20.000037
ORF1ab/nsp12253A253VgCAgTT11AY.960.002075
ORF1ab/nsp12253A253VgCagTa11AY.980.000079
ORF1ab/nsp12253A253SGcaTca11AY.980.000079
ORF1ab/nsp12253A253SGcaTca11B0.000128
ORF1ab/nsp12253A253del1gcAgc-11B.10.000009
ORF1ab/nsp12253A253AgcAgcG11B.1.10.000018
ORF1ab/nsp12253A253VgCagTa11B.1.10.000018
ORF1ab/nsp12253A253delGCA---11B.1.10.000018
ORF1ab/nsp12253A253delGCA---11B.1.1.10.000327
ORF1ab/nsp12253A253AgcAgcG11B.1.1.2070.001182
ORF1ab/nsp12253A253AgcAgcG11B.1.1.2140.000055
ORF1ab/nsp12253A253VgCagTa11B.1.1.2160.00089
ORF1ab/nsp12253A253VgCagTa11B.1.1.2220.000204
ORF1ab/nsp12253A253PGcaCca11B.1.1.3070.002532
ORF1ab/nsp12253A253AgcAgcG11B.1.1.3150.008475
ORF1ab/nsp12253A253AgcAgcG11B.1.1.3350.012987
ORF1ab/nsp12253A253SGcaTca11B.1.1.3690.000446
ORF1ab/nsp12253A253AgcAgcT11B.1.1.370.000193
ORF1ab/nsp12253A253AgcAgcG11B.1.1.3750.011905
ORF1ab/nsp12253A253TGcaAca11B.1.1.390.00051
ORF1ab/nsp12253A253VgCagTa11B.1.1.4160.000905
ORF1ab/nsp12253A253SGcaTca11B.1.1.5190.00004
ORF1ab/nsp12253A253del1gcAgc-11B.1.1600.000031
ORF1ab/nsp12253A253AgcAgcG11B.1.160.160.000929
ORF1ab/nsp12253A253SGcaTca11B.1.177.260.006993
ORF1ab/nsp12253A253SGcaTca11B.1.177.540.000606
ORF1ab/nsp12253A253SGcaTca11B.1.20.000009
ORF1ab/nsp12253A253PGcaCca11B.1.20.000009
ORF1ab/nsp12253A253TGcaAca11B.1.2210.000071
ORF1ab/nsp12253A253del1gCag-a11B.1.2210.000071
ORF1ab/nsp12253A253TGcaAca11B.1.2430.00007
ORF1ab/nsp12253A253AgcAgcG11B.1.2580.000067
ORF1ab/nsp12253A253VgCagTa11B.1.3240.001605
ORF1ab/nsp12253A253AgcAgcG11B.1.3500.002933
ORF1ab/nsp12253A253AgcAgcG11B.1.3510.00003
ORF1ab/nsp12253A253PGcaCca11B.1.3560.001727
ORF1ab/nsp12253A253SGcaTca11B.1.36.390.002217
ORF1ab/nsp12253A253VgCagTa11B.1.4270.00005
ORF1ab/nsp12253A253del1Gca-ca11B.1.4290.000024
ORF1ab/nsp12253A253SGcaTca11B.1.4340.052632
ORF1ab/nsp12253A253AgcAgcT11B.1.4590.004082
ORF1ab/nsp12253A253AgcAgcG11B.1.4740.001901
ORF1ab/nsp12253A253SGcaTca11B.1.5230.002451
ORF1ab/nsp12253A253delGCA---11B.1.5250.000113
ORF1ab/nsp12253A253AgcAgcG11B.1.5260.000024
ORF1ab/nsp12253A253EgCagAa11B.1.5460.003704
ORF1ab/nsp12253A253AgcAgcG11B.1.5770.000687
ORF1ab/nsp12253A253VgCagTa11B.1.5880.00091
ORF1ab/nsp12253A253PGcaCca11B.1.617.10.000129
ORF1ab/nsp12253A253VgCagTa11B.1.617.10.000129
ORF1ab/nsp12253A253TGcaAca11B.270.015385
ORF1ab/nsp12253A253SGcaTca11B.290.003509
ORF1ab/nsp12253A253SGcaTca11B.30.000831
ORF1ab/nsp12253A253GgCagGa11B.60.00091
ORF1ab/nsp12253A253AgcAgcG11B.6.60.000889
ORF1ab/nsp12253A253VgCagTa11C.10.002392
ORF1ab/nsp12253A253SGcaTca11C.10.002392
ORF1ab/nsp12253A253VgCagTa11D.20.000075
ORF1ab/nsp12253A253SGcaTca11D.30.005917
ORF1ab/nsp12253A253TGcaAca11P.10.000016
ORF1ab/nsp12253A253VgCagTa11P.1.140.000048
ORF1ab/nsp12253A253AgcAgcG11P.1.140.000048
ORF1ab/nsp12253A253AgcAgcG11Q.10.000126

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.