COVID-19 Viral Genome Analysis Pipeline
Enabled by data from
Embers
Embers: follow emergent SARS-CoV-2 variants over time
Last update: Sep 12, 2021
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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%
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last modified: Tue Jun 22 15:04 2021
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Questions or comments? Contact us at seq-info@lanl.gov.
Questions or comments? Contact us at seq-info@lanl.gov.
