COVID-19 Viral Genome Analysis Pipeline
Enabled by data from
Embers
Embers: follow emergent SARS-CoV-2 variants over time
Run Geographically Restricted Embers
Last update: Dec 3, 2021
Delta Variants
Global
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Variants and Counts
11111
111111111122222222222222223444445566666667789900112
11222677789134445555912444444455555894157890711577780155827176
89069905605282452678052234678901238996728401034557911690274864
LTTPTHVGTDTSDGYYWEFRRDALALRSYLTPGDWVTRKLTEFNAQDHQQNPATTDSTNDVV Counts Percent Lineage
.R...._..........G--.._..........._..._RKQ....G____R...N....._ 2688 0.14% Delta+E484Q
.R...._..........--G.._..........._..._RKQ....G____R...N....._ 0 0.00% Delta+E484Q
.R...._..........--G.............._..._RK.....G...*....N...... 0 0.00% Delta+FurinRelated
.R...._..........--G.............._..._RK.....G..*.....N...... 0 0.00% Delta+FurinRelated
.R...._..........--G.............._..._RK.....G.*......N...... 0 0.00% Delta+FurinRelated
.R...._..........--G.............._..._RK.....G....H...N...... 0 0.00% Delta+FurinRelated
.R...._..........--G.............._..._RK.....GY.......N...... 0 0.00% Delta+FurinRelated
.R...._..........G--.............._..._RK.....G...*....N...... 709 0.04% Delta+FurinRelated
.R...._..........G--.............._..._RK.....G..*.....N...... 10048 0.54% Delta+FurinRelated
.R...._..........G--.............._..._RK.....G.*......N...... 5985 0.32% Delta+FurinRelated
.R...._..........G--.............._..._RK.....G....H...N...... 407 0.02% Delta+FurinRelated
.R...._..........G--.............._..._RK.....GY.......N...... 1680 0.09% Delta+FurinRelated
.R...._..._......G--..V..........._I.._RK.....G____R...N....._ 20928 1.12% Delta+T95_,A222V,V289I
.R...._..._......--G..V..........._I.._RK.....G____R...N....._ 0 0.00% Delta+T95_,A222V,V289I
.R...._..._......G--.._........L.._..._RK_....G____R...N....._ 13057 0.70% Delta+T95_,P251L
.R...._..._......--G.._........L.._..._RK_....G____R...N....._ 0 0.00% Delta+T95_,P251L
.R...._...I....H.G--.............._..._RK.....G____R...N.....L 8372 0.45% Delta+Y145H,V1264L
.R...._...I....H.--G.............._..._RK.....G____R...N.....L 0 0.00% Delta+Y145H,V1264L
.R...._...I....H.G--..V..........._..._RK.....G____R...N....._ 41373 2.20% Delta+Y145H,A222V
.R...._...I....H.--G..V..........._..._RK.....G____R...N....._ 0 0.00% Delta+Y145H,A222V
.R....F..........G--..V..........._...NRK.....G........N...... 1343 0.07% Delta+T95_,V70F,A222V,K417N
.R....F..........--G..V..........._...NRK.....G........N...... 0 0.00% Delta+T95_,V70F,A222V,K417N
.R..A._..._......--G.._.......I..._.I._RK_...HG____R...N....._ 0 0.00% Delta+T29A,T95_,T250I,T299I,Q613H
.R..A._..._......G--.._.......I..._.I._RK_...HG____R...N....._ 2997 0.16% Delta+T29A,T95_,T250I,T299I,Q613H
.R..A._..._......G--.._.......I..._._._RK_..._G____R...N....._ 3666 0.20% Delta+T29A,T95_,T250I
.R..A._..._......--G.._.......I..._._._RK_..._G____R...N....._ 0 0.00% Delta+T29A,T95_,T250I
.R...._..........G--.............._..._RK.....G____R...N..S..L 7969 0.42% Delta+N1074S,V1264L
.R...._..........--G.............._..._RK.....G____R...N..S..L 0 0.00% Delta+N1074S,V1264L
.R...._........_.G--.............._..._RK.....G____R...N.._..L 27478 1.46% Delta+V1264L
.R...._........_.--G.............._..._RK.....G____R...N.._..L 0 0.00% Delta+V1264L
.R.........L.....G--.._..........._..._RK_....G____R...N....._ 38595 2.06% Delta+S112L
.R.........L.....--G.._..........._..._RK_....G____R...N....._ 1 0.00% Delta+S112L
.R...._..._......G--..V...........__.._RK.....G____R...N....._ 85041 4.53% Delta+T95_,A222V
.R...._..._......--G..V...........__.._RK.....G____R...N....._ 1 0.00% Delta+T95_,A222V
.R.._._...._.....G--.._.......__.._._._RK_..._G____R...N....._ 1398815 74.53% Delta
.R.._._...._.....--G.._.......__.._._._RK_..._G____R...N....._ 24 0.00% Delta
....................S....................K.Y..GY...*........F. 3832 0.20% Gamma+FurinRelated
....................S....................K.Y..GY..*.........F. 1499 0.08% Gamma+FurinRelated
....................S....................K.Y..GY.*..........F. 296 0.02% Gamma+FurinRelated
....................S....................K.Y..GY*...........F. 800 0.04% Gamma+FurinRelated
....................S....................K.Y..GY____........F. 27541 1.47% Gamma
..........I...SN.....................K...K.Y..G....H...N...... 4698 0.25% Mu
.......VI..................-------.....Q..S...G.......N....... 3480 0.19% Lambda
.........A...........G.---............N..K.Y..G.....V......... 783 0.04% Beta
.._..--.......-._........................_SYD.G....H.I..A..H.. 507 0.03% Alpha+F490S
.._..--.......-..........................K.YD.G....H.I..A..H.. 734 0.04% Alpha+E484K
.._..--.......-._........................__YD.G....H._..A..H.. 136 0.01% Alpha
.._..--.......-._........................__YD.G....R.I..A..H.. 72 0.00% Alpha
.._..--......._._........................__YD.G....H.I..A..H.. 277 0.01% Alpha
.._..--.......-._........................__YD.G....H.I..A..H.. 62942 3.35% Alpha
The most common sequence patterns that are missed by the varint patterns
Missing: 4134 patterns, for a total of 98099 sequences
11111
111111111122222222222222223444445566666667789900112
11222677789134445555912444444455555894157890711577780155827176
89069905605282452678052234678901238996728401034557911690274864
LTTPTHVGTDTSDGYYWEFRRDALALRSYLTPGDWVTRKLTEFNAQDHQQNPATTDSTNDVV Counts Percent NearbyLineage(s)
_R_______________G--___________________RK_____G____R__________ 10809 0.58%
_R________I______G--___________________RK_____G____R__________ 5258 0.28%
_R____I______D___G--___________________RK_____G____R___N______ 4866 0.26%
_R___________D___G--___________________RK____HG____R___N______ 3947 0.21%
______________________________________________G_______________ 3493 0.19%
_R____I__________G--___________________RK_____G____R___N______ 2792 0.15%
_R_____________________________________RK_____G____R___N______ 2520 0.13%
_R____F___I__D___G--___________________RK_____G____R___N______ 2177 0.12%
_R_______________G--__V________________RK_____G____R__________ 2008 0.11%
_____--_______-_R__________________________YD_G____H_I__A__H__ 1930 0.10%
_R___________D___G--______________R____RK_____G____R___N______ 1886 0.10%
_______________________________________RK_____G____R___N______ 1340 0.07%
_R___________D___G--___________________RK_____G____R__________ 1335 0.07%
_________________________________________K____G__________I____ 1215 0.06%
R_________I________S__________________________G____H_____I____ 1153 0.06%
_R________I__D___G--___________________RK____HG____R___N______ 1134 0.06%
_R__I_____I__D___G--___________________RK_____G____R___N______ 1042 0.06%
_R___________D___G--______________L____RK_____G____R___N______ 1019 0.05%
_R__A________D___G--__________I________RK____HG____R___N______ 955 0.05%
_R_______________G--___________________RK____HG____R___N______ 882 0.05%
___________________________________________Y__G_______________ 801 0.04%
_R________I__D___G--______________L___NRK_____G____R___N______ 751 0.04%
_R________I____________________________RK_____G____R___N______ 734 0.04%
_R________I__D___G--__V________________RK_____G____R___N______ 723 0.04%
_R________I__D___G--______________L____RK_____G____R___N______ 647 0.03%
__________I______________________G_______K____G_____V_________ 640 0.03%
__________I___-__________________________K____G____H__________ 612 0.03%
_R___________D___G--__S________________RK_____G____R___N______ 585 0.03%
_________G____-___S____________________R______G_______NH______ 577 0.03%
_R_______________G--____________________K_____G____R___N______ 565 0.03%
_R________I______G--__V________________RK_____G____R___N______ 528 0.03%
_R____F______D___G--___________________RK_____G____R___N______ 521 0.03%
_____________D___G--___________________RK_____G____R___N______ 515 0.03%
_R_______________________________________K____G________N______ 505 0.03%
_R________I__D___G--___________________RK_____G____R__________ 483 0.03%
_R_________L_____G--___________________RK_____G____R__________ 482 0.03%
_R________I__D___G--__S________________RK_____G____R___N______ 475 0.03%
_R________I__D___G--__________I________RK_____G____R___N______ 461 0.02%
_R__I________D___G--___________________RK_____G____R___N______ 446 0.02%
_R___________D_________________________RK_____G____R___N______ 442 0.02%
_R___________D___G--____________________K_____G____R___N______ 431 0.02%
________________________________________K_____G____H__________ 419 0.02%
_R_______________G--___________________RK___S_G____R__________ 405 0.02%
_R___--__________G--___________________RK_____G____R___N______ 368 0.02%
_R___________D___G--________________I__RK_____G____R___N______ 368 0.02%
_R_______________G--__V____________I___RK_____G____R__________ 360 0.02%
______________________________________________G____R__________ 360 0.02%
_R________I__D___G--__________N________RK_____G____R___N______ 355 0.02%
_R________I__D_________________________RK_____G____R___N______ 340 0.02%
_____--_________R____________________S_R______G__H____________ 327 0.02%
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last modified: Sat Nov 13 13:34 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.
