COVID-19 Viral Genome Analysis Pipeline
Enabled by data from
Embers
Embers: follow emergent SARS-CoV-2 variants over time
Last update: Jul 31, 2021
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Variants and Counts
111111
1111111111112222222222222223334444444444556666666777777788888999001112
111122566777892344455555891244444444555550461135577899071155778013678935589558271171
5238906279056056823424678905223456789012386674790278404103435571162920694989072711869
LSSLTTPQAHVGTDTVDGVYWEEFRLRDALALHRSYLTPGDWFRVQKNNLSTEFSNAQDAHQQPATTGVEDDKTFADQSTQEDVG Counts Percent Lineage
_____________________________________________________________________________________ 386 0.03% Ancestral
._________________________________________________________G__________________________ 48457 4.02% G-clade
.__.________________________V_____________________________G__________________________ 24124 2.00% GV-clade
._________________________________________________________G____*_____________________ 4265 0.35% Near-Furin
__________________________________________________________G___*______________________ 6346 0.53% Near-Furin
__________________________________________________________G__*_______________________ 4675 0.39% Near-Furin
....._...--........-_...............................__.YD.G....H.I............A...H.. 723786 60.06% B.1.1.7=Alpha
....._...--........-R..................................YD.G....H.I............A...H.. 12394 1.03% Alpha+W152R
....._...--........-................................K..YD.G....H.I............A...H.. 2056 0.17% Alpha+E484K
....._...--........-_..............................._S.YD.G....H.I............A...H.. 2842 0.24% Alpha+F490S
.....I...--........-_..............................._..YD.G....H.I............A...H.. 2350 0.19% Alpha+T20I
.............A.............G.---..............N.....K..Y..G.....V.................... 7271 0.60% B.1.351=Beta
.....NS.........Y.........S.........................K..Y..G.Y..................I...F. 42185 3.50% P.1=Gamma
....R....._...........--G..._............_...._..R.K......G....R............N........ 124524 10.33% B.1.617.2=Delta
....R....._...........--G...V............_...._..R.K......G....R............N........ 14778 1.23% B.1.617.2=Delta+A222V
....R.....F...........--G...V............_....N..R.K......G....R............N........ 393 0.03% B.1.617.2=AY.2
....R....._...I.......--G................L....N..R.K......G....R............N........ 198 0.02% B.1.617.2=AY.1
..I.................C............................R........G.......................... 20591 1.71% B.1.429/7=Epsilon
.............._..............................._.....K.._..G..............._........F. 2171 0.18% P.2=Zeta
.......RV--........-................................K.....G...H...........L.......... 4293 0.36% B.1.525=Eta
..............I.........................G.................G.....V............_....... 20186 1.67% B.1.526=Iota
..............I.........................G.........N.......G....._............R....... 9355 0.78% B.1.526.2
.............G.....-...S.........................R........G..............N..H........ 8012 0.66% B.1.526.1
......................___........................R..Q.....G....R..................... 2797 0.23% B.1.617.1=Kappa
...........VI.....................------.........Q...S....G..............N........... 2331 0.19% C.37=Lambda
.................................................R.....Y.._VY.........Y.............V 317 0.03% A.27
.......................L....................F............H_....R..................... 400 0.03% A.23.1
...................................................K......G....H..A.................. 16546 1.37% B.1.1.519
....................L...............................K.....G........V................. 7990 0.66% R.1
......................................................P_..G....H.I............_..._.. 2459 0.20% B.1.575
.........--..............F.....................K..........G.........I................ 4035 0.33% B.1.258.17
.._..............--........._....................R.._.....G.............._.._........ 619 0.05% A.2.5.2
.............................................K..K.........G......I................... 1089 0.09% B.1.214.2
.F.......--.........R......................S.....R........G...H............S......... 1056 0.09% C.36
......................---.................L.........K.P...G..........A.V.......I..... 251 0.02% B.1.1.523
......S..--....A...-.........---Y.................N.K.....G....H...............I..H.. 536 0.04% B.1.620
......................................................PY..G....H........N........K... 599 0.05% B.1.623
..............I....-................................K.....G....H......H.............. 2821 0.23% B.1.1.318
The most common sequence patterns that are missed by the varint patterns
111111
1111111111112222222222222223334444444444556666666777777788888999001112
111122566777892344455555891244444444555550461135577899071155778013678935589558271171
5238906279056056823424678905223456789012386674790278404103435571162920694989072711869
LSSLTTPQAHVGTDTVDGVYWEEFRLRDALALHRSYLTPGDWFRVQKNNLSTEFSNAQDAHQQPATTGVEDDKTFADQSTQEDVG Counts Percent NearbyLineage(s)
__________________________________________________N_______G__________________________ 6380 0.53% G-clade
____________________________________________________K_____G____________________I_____ 1966 0.16% P.2=Zeta
_______________________________________________________Y__G__________________________ 1853 0.15% G-clade
_________--____________________________________K__________G__________________________ 1844 0.15%
_______________________________________________K__________G__________________________ 1554 0.13% G-clade
_________--________-___________________________________YD_G____R_I____________A___H__ 1471 0.12% B.1.1.7=Alpha
_________--____________________________________________YD_G____H_I____________A___H__ 1389 0.12% B.1.1.7=Alpha
_________-F________-___________________________________YD_G____H_I____________A___H__ 1157 0.10% B.1.1.7=Alpha
__________________________________________________________GV_H_______________________ 1126 0.09%
_______________________________________________K__________G____R_____________________ 1088 0.09%
___F______________________________________________________G__________Q_______________ 1028 0.09%
________________Y_________________________________________G__________________________ 977 0.08% G-clade
__________________________________________________________G_______A__________________ 887 0.07% G-clade
___F_NS___________________S___________________T_____K__Y__G_Y__________________I___F_ 871 0.07% P.1=Gamma
______________I____S_______________________K________K__Y__G____H____________N________ 818 0.07%
___F______________________________________________________G__________________________ 816 0.07% G-clade, GV-clade
________________Y_________________________________N_______G__R_______________________ 777 0.06%
_____I____________________________________________________G__________________________ 775 0.06% G-clade
_________--________-___________________________________YD_G____H______________A___H__ 753 0.06% B.1.1.7=Alpha
_______________________________________________________T__G__________________________ 750 0.06% G-clade
_________________________________________________R________G__________________________ 704 0.06% G-clade
__________________________________________________N_______G__H_______________________ 661 0.05%
____________________________V_____________________________G__H_______________________ 613 0.05% GV-clade
F________--________-___________________________________YD_G____H_I____________A___Y__ 598 0.05% B.1.1.7=Alpha
_________--_______-F___________________________________YD_G____H_I____________A___H__ 546 0.05% B.1.1.7=Alpha
_______________________________________________________YD_G____H_I____________A___H__ 516 0.04%
____________________________V_____________________________G_____________________L____ 477 0.04% GV-clade
______________________________________________________P___G__________________________ 464 0.04% G-clade
_________--________-____________________________________D_G____H_I____________A___H__ 427 0.04% B.1.1.7=Alpha
_________________S________________________________________G___H______________________ 403 0.03%
F_________________________________________________________G___H______________________ 402 0.03% G-clade
__________________________________________________________G________________________F_ 389 0.03% G-clade, P.2=Zeta
____R_____F___I__D____--G________________________R_K______G____R____________N________ 389 0.03% B.1.617.2=Delta
_________--________-_________________________________L_YD_G____H_I____________A___H__ 388 0.03% B.1.1.7=Alpha, Alpha+W152R, Alpha+E484K, Alpha+F490S, Alpha+T20I
_F________________________________________________________G__________________________ 360 0.03% G-clade
___R__________I_________S_________________________________G____H_______________I_____ 335 0.03%
______________________________________________________PY__G____H_________________K___ 333 0.03% B.1.623
_________--________-___________________________________YD_G____H_I________________H__ 329 0.03% B.1.1.7=Alpha
_________--_______________________________________________G__________________________ 324 0.03%
____R_________I_______--G________________________R_K______G____R_____________________ 320 0.03% B.1.617.2=Delta
____________________________________________________K_____G__________________________ 316 0.03% G-clade, P.2=Zeta
____R____________________________________________R_K______G____R____________N________ 314 0.03% B.1.617.1=Kappa
_F_______________________________________________R________G___H______________________ 310 0.03%
__________________________________________________________G________V_________________ 309 0.03% G-clade
__________________________________________________________G_____V____________________ 289 0.02% G-clade
______________I___________________________________________G__________________________ 271 0.02% G-clade
_________--________-___________________________________Y__G____H_I____________A___H__ 267 0.02% B.1.1.7=Alpha
__________________________________________________________G___H___S__________________ 261 0.02%
_________________________________________________Q________G__________________________ 260 0.02% G-clade
____R_________________--G________________________R_K______G____R_____________________ 255 0.02% B.1.617.2=Delta
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last modified: Tue Jun 22 15:04 2021
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