COVID-19 Viral Genome Analysis Pipeline COVID-19 Viral Genome Analysis Pipeline home COVID-19 Viral Genome Analysis Pipeline home
COVID-19 Viral Genome Analysis Pipeline
Enabled by data from   gisaid-logo


Embers

Embers: follow emergent SARS-CoV-2 variants over time

Last update: Sep 12, 2021
Run Geographically Restricted Embers
Download

Global
Variants color key

Variants and Counts
                                                                                    111111
               111111111111122222222222222223334444444444455666666677777778888899999001112
 11112256677789234444555558911244444444555550461134557789907115577801367893558933558271171
523890627905605682345246789005223456789012386674790027840410343557116292069498969072711869
LSSLTTPQAHVGTDTVDGVYYWEEFRLRIDALALHRSYLTPGDWFRVQKNNNLSTEFSNAQDAHQQPATTGVEDDKTFADSDQSTQEDVG Counts Percent Lineage
..............I....SN........................K.........K..Y..G....H..............N........   2507   0.19% B.1.621          
............................T.....................K....K.....G.................NF...I.....   2438   0.18% B.1.619          
..............I....-...................................K.....G....H......H................   2892   0.22% B.1.1.318        
.........................................................PY..G....H........N..........K...    587   0.04% B.1.623          
......S..--....A...-...........---Y..................N.K.....G....H.................I..H..    594   0.05% B.1.620          
.......................---..................L..........K.P...G..........A.V.........I.....      0   0.00% B.1.1.523        
.F.......--..........R.......................S......R........G...H............S...........   1105   0.08% C.36             
...............................................K...K.........G......I.....................    683   0.05% B.1.214.2        
.._..............--..........._.....................R.._.....G...__........._...._........     28   0.00% A.2.5.2          
.........--...............F......................K...........G.........I..................   1578   0.12% B.1.258.17       
.........................................................P_..G....H.I.............._..._..   1738   0.13% B.1.575          
.....................L.................................K.....G........V...................   7253   0.55% R.1              
......................................................K......G....H..A....................  12216   0.93% B.1.1.519        
........................L.....................F.............H_....R.......................    142   0.01% A23.1            
....................................................R.....Y.._VY.........Y...............V    102   0.01% A.27             
...........VI.......................-------.........Q...S....G..............N.............   3435   0.26% C.37=Lambda      
.......................___..........................R..Q.....G....R.......................   2495   0.19% B.1.617.1=Kappa  
.............G.....-....S...........................R........G..............N....H........   7641   0.58% B.1.526.1        
..............I...........................G..........N.......G....._..............R.......   8683   0.66% B.1.526.2        
..............I...........................G..................G.....V.............._.......  18360   1.39% B.1.526=Iota     
.......RV--........-...................................K.....G...H...........L............   3067   0.23% B.1.525=Eta      
.............._................................._......K.._..G..............._..........F.    739   0.06% P.2=Zeta         
..I..................C..............................R........G............................  13342   1.01% B.1.429/7=Epsilon
....R....._...I........G--.................L....N...R.K......G....R..............N........    414   0.03% Delta-AY.1       
....R....._...I........--G.................L....N...R.K......G....R..............N........      0   0.00% Delta-AY.1       
....R.....F............G--....V............_....N...R.K......G....R..............N........    865   0.07% Delta-AY.2       
....R.....F............--G....V............_....N...R.K......G....R..............N........      0   0.00% Delta-AY.2       
....R....._............G--....V............_...._...R.K......G....R..............N........  48116   3.65% Delta+A222V      
....R....._............--G....V............_...._...R.K......G....R..............N........      0   0.00% Delta+A222V      
....R....._............G--...._............_...._...R.K......G....R..............N........ 397179  30.12% B.1.617.2=Delta  
....R....._............--G...._............_...._...R.K......G....R..............N........      7   0.00% B.1.617.2=Delta  
.....NS....................S...........................K..Y..G.Y....................I...F.  54937   4.17% P.1=Gamma        
.............A...............G.---..............N......K..Y..G.....V......................   5725   0.43% B.1.351=Beta     
.....I...--........-._................................._..YD.G....H.I..............A...H..   2224   0.17% Alpha+T20I       
....._...--........-._................................._S.YD.G....H.I..............A...H..   2767   0.21% Alpha+F490S      
....._...--........-...................................K..YD.G....H.I..............A...H..   2235   0.17% Alpha+E484K      
....._...--........-.R....................................YD.G....H.I..............A...H..  11558   0.88% Alpha+W152R      
....._...--........-._.................................__.YD.G....H._..............A...H..    666   0.05% B.1.1.7=Alpha    
....._...--........-._.................................__.YD.G....R.I..............A...H..   1402   0.11% B.1.1.7=Alpha    
....._...--........_._.................................__.YD.G....H.I..............A...H..   1344   0.10% B.1.1.7=Alpha    
....._...--........-._.................................__.YD.G....H.I..............A...H.. 613538  46.53% B.1.1.7=Alpha    
_____________________________________________________________G__*_________________________   1750   0.13% Near-Furin       
_____________________________________________________________G___*________________________   1764   0.13% Near-Furin       
.____________________________________________________________G____*_______________________    912   0.07% Near-Furin       
.__.__________________________V______________________________G____________________________   2570   0.19% GV-clade         
._______________Y____________________________________________G____________________________    115   0.01% G-clade          
.____I_______________________________________________________G____________________________    105   0.01% G-clade          
.____________________________________________________________G_______A____________________    179   0.01% G-clade          
.________________________________________________K___________G____________________________    247   0.02% G-clade          
._________________________________________________________*__G____________________________   2047   0.16% G-clade          
.____________________________________________________N_______G____________________________    827   0.06% G-clade          
.____________________________________________________________G____________________________  11731   0.89% G-clade          
__________________________________________________________________________________________    137   0.01% Ancestral        


The most common sequence patterns that are missed by the varint patterns
Missing: 5615 patterns, for a total of 12464 sequences
                                                                                    111111
               111111111111122222222222222223334444444444455666666677777778888899999001112
 11112256677789234444555558911244444444555550461134557789907115577801367893558933558271171
523890627905605682345246789005223456789012386674790027840410343557116292069498969072711869
LSSLTTPQAHVGTDTVDGVYYWEEFRLRIDALALHRSYLTPGDWFRVQKNNNLSTEFSNAQDAHQQPATTGVEDDKTFADSDQSTQEDVG Counts Percent NearbyLineage(s)
____R__________________________________________________K_____G___________________N________    500   0.04% 
____R_____________________________________________________Y__G____________________________    291   0.02% 
____R_____________________________________________________Y__G___________________N________    261   0.02% 
____________________________________________________R________G____R_______________________    233   0.02% 
____R____________D_____G-___________________________R_K______G____R______________N________    177   0.01% 
__________________________________________________________Y__G___________________N________    162   0.01% 
_______________________________---________________________Y__G____________________________    124   0.01% 
____R_____________________________________________________Y__G____R______________N________    122   0.01% 
____________________________________________________R_K______G____R_______________________     66   0.01% 
_____________________________________________________________G_______________L____________     66   0.01% 
________________________________________________N____________G____________________________     57   0.00% 
_____________________________________________________________G___________________N________     53   0.00% 
_________--________-______________________________________YD_G____HVI______________A______     43   0.00% 
_________--_______F______________________________K___________G____________________________     41   0.00% 
____R_______________________________________________R_K___Y__G____R______________N________     37   0.00% 
____R_____________________________________________________Y__G____R_______________________     37   0.00% 
_________--________-______________________________________Y__G______I______________A______     34   0.00% 
_______________________________________________________K_____G__H_________________________     33   0.00% 
_________________D_____G--__________________________R_K___Y__G____R______________N________     30   0.00% 
____R_________I__D_____G--__________________________R_K___Y__G____H______________N________     30   0.00% B.1.1.519
F__F__S______________________________________________________G___H________________________     30   0.00% 
_________--________-______________________________________Y__G______I_____________________     30   0.00% 
____R____________D_____G--_____________I____________R_K______G___________________N________     28   0.00% 
__________________________________________________________Y__G______I_____________________     28   0.00% 
__________________________________________________________Y__G____R_______________________     26   0.00% 
________________H____________________________________N_______G____________________________     25   0.00% 
______________________________________________________K______G____________________________     25   0.00% 
______________I____S_________________________K_________K__Y__G____H______________N________     25   0.00% B.1.621
____R_______________________________________________R_KK__Y__G____R______________N________     25   0.00% 
F__F__S___________________________________________K__________G___H________________________     25   0.00% 
___________________________________________________________S_G__H_________________________     25   0.00% 
________________________________________________N______K__Y__G____________________________     24   0.00% 
____R_________I_________--__________________________R_K______G____R______________N________     22   0.00% 
_________--________-______________________________________YD______H_I__________________H__     22   0.00% 
__________________________________________G____________K__Y__G____________________________     22   0.00% 
____________I_________________V______________________________G____________________________     22   0.00% 
____R__________________G--____________________________K___Y__G____R______________N________     21   0.00% 
___________________-___________________________________K_____G___H________________________     21   0.00% 
___F__S___________________________________________K__________G___H________________________     21   0.00% 
____R__________________G--____S_____________________R_K______G____R______________N________     20   0.00% 
F__F_________________________________________________________G__________Q_______________F_     20   0.00% 
_________--_______________________________________________TV___Y__________________________     20   0.00% 
_________Q___________________________________________________G____________________________     19   0.00% 
___F_______V__________________V______________________________G____________________________     19   0.00% 
____R_________________________________________________K______G____R______________N________     19   0.00% 
____R_________I____SN_-_______________________________K______G___________________N________     19   0.00% 
_____________________________________________________________G____R______________N________     19   0.00% 
_____________________________HV______________________________G__H_________________________     19   0.00% 
____R_________I______________________________________________G____________________________     19   0.00% 
_________--________-_S____________________________________YD_G____H_I______________A___H__     18   0.00% 

Download

 

last modified: Tue Jun 22 15:04 2021



GISAID data provided on this website is subject to GISAID's Terms and Conditions
Questions or comments? Contact us at seq-info@lanl.gov.

 
Operated by Triad National Security, LLC for the U.S. Department of Energy's National Nuclear Security Administration
© Copyright Triad National Security, LLC. All Rights Reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health