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: Feb 3, 2023
Delta and Omicron Variants
Global
| Frequencies of Key Pango Lineage Groupings Over Time |
 |
 |
Variants and Counts
1111
1111111111222222222222222222222222223333334444444444444455556666667777788999990112
1122222266777893444455559111111111112444444455555893477770014457788999900471577780016955556882176
8904567979056058234526780122223444452234678901238999613565870627846036815704557911464669049127864
LTTLPPATAHVGTDTDGVYYWEFRRNL---VR---DALALRSYLTPGDWVTGRSSSTDRKNGLSTEFFQGQNYTADHQQNPASTNDNTDQNLSTDVV Counts Percent Lineage
.I..............D..........SGRG.---................D.FPFANSNK._NKA..R.RYH..GY..KH...KY...HK...... 3 0.00% Omicron_BA.2+212SGR
.I.........................---G.---................D.FPFANSNK.RNKAV._.RYH..GY..KH...KY...HK...... 1008180 85.78% Omicron_BA.4andBA.5
.I..............D..........---G.---................D.FPFANSNK.QNKA..R.RYH..GY..KH.L.KY...HK...... 1849 0.16% Omicron_BA.2+L452Q+S704L_BA.2.12.1
.I..__..........D..........---G.---................D.FPFANSNK._NKA..R.RYH..GY..KH...KY...HK...... 5 0.00% Omicron_BA.2+P25_,P26_
.I..--..........D..........---G.---................D.FPFANSN..MNKA..R.RYH..GY..KH...KY...HK...... 301 0.03% Omicron_BA.2+L452M
.I..............D..........---G.---................D.FPFANSTK..NKA..R.RYH..GY..KH...KY...HK...... 349 0.03% Omicron_BA.2+K417T
.I..--..........D..........---G.---................D.FPFANSN.._NKA..R.RYH..GY..KH...KY...HK...... 2400 0.20% Omicron_BA.2
........V--...I............---..---................DKLPF.........A..R.RYH..GY..KH...KY...HK...... 95 0.01% Omicron_BA.1.1
........V--...I............---..---................D_.PF___..._..A..R.RYHK.GY..KH...KYK..HKF..... 10 0.00% Omicron_BA.1
........V--...I............---..EPE................D_.PF......_..A..R.RYH..GY..KH...KY...HK...... 57 0.00% Omicron_BA.1
.R........_..........--G...---..---............._.........._..R.K..........G...*........N........ 0 0.00% Delta+FurinRelated
.R........_..........--G...---..---............._.........._..R.K..........G..*.........N........ 0 0.00% Delta+FurinRelated
.R........_..........--G...---..---............._.........._..R.K..........G.*..........N........ 0 0.00% Delta+FurinRelated
.R........_..........--G...---..---............._.........._..R.K..........G....H.......N........ 0 0.00% Delta+FurinRelated
.R........_..........--G...---..---............._.........._..R.K..........GY...........N........ 0 0.00% Delta+FurinRelated
.R........_..........G--...---..---............._.........._..R.K..........G...*........N........ 0 0.00% Delta+FurinRelated
.R........_..........G--...---..---............._.........._..R.K..........G..*.........N........ 1 0.00% Delta+FurinRelated
.R........_..........G--...---..---............._.........._..R.K..........G.*..........N........ 0 0.00% Delta+FurinRelated
.R........_..........G--...---..---............._.........._..R.K..........G....H.......N........ 0 0.00% Delta+FurinRelated
.R........_..........G--...---..---............._.........._..R.K..........GY...........N........ 0 0.00% Delta+FurinRelated
.R........_...I....H.G--...---..---.V..........._.........._..R.K..........G____R.......N........ 0 0.00% Delta+Y145H,A222V
.R........_...I....H.--G...---..---.V..........._.........._..R.K..........G____R.......N........ 0 0.00% Delta+Y145H,A222V
.R........_..._......G--...---..---.V...........__........._..R.K..........G____R.......N......._ 1 0.00% Delta+T95_,A222V
.R........_..._......--G...---..---.V...........__........._..R.K..........G____R.......N......._ 0 0.00% Delta+T95_,A222V
.R....._.._..........G--...---..---._.......__.._._........_..R.K_.........G____R.......N......._ 30 0.00% Delta
.R....._.._..........--G...---..---._.......__.._._........_..R.K_.........G____R.......N......._ 0 0.00% Delta
........................S..---..---..............................K.....Y...GY...*..............F. 0 0.00% Gamma+FurinRelated
........................S..---..---..............................K.....Y...GY..*...............F. 0 0.00% Gamma+FurinRelated
........................S..---..---..............................K.....Y...GY.*................F. 0 0.00% Gamma+FurinRelated
........................S..---..---..............................K.....Y...GY*.................F. 0 0.00% Gamma+FurinRelated
........................S..---..---..............................K.....Y...GY____..............F. 0 0.00% Gamma
..............I...SN.......---..---.................K............K.....Y...G....H.......N........ 0 0.00% Mu
...........VI..............---..---......-------..............Q....S.......G...........N......... 0 0.00% Lambda
.............A.............---..---G.---...................N.....K.....Y...G.....V............... 1 0.00% Beta
.._......--.......-._......---..---....................................Y..DG....H.._........A.H.. 0 0.00% Alpha
.._......--.......-._......---..---....................................Y..DG....R..I........A.H.. 0 0.00% Alpha
.._......--......._._......---..---....................................Y..DG....H..I........A.H.. 0 0.00% Alpha
.._......--.......-._......---..---....................................Y..DG....H..I........A.H.. 1 0.00% Alpha
The most common sequence patterns that are missed by the varint patterns
Missing: 7353 patterns, for a total of 162088 sequences
1111
1111111111222222222222222222222222223333334444444444444455556666667777788999990112
1122222266777893444455559111111111112444444455555893477770014457788999900471577780016955556882176
8904567979056058234526780122223444452234678901238999613565870627846036815704557911464669049127864
LTTLPPATAHVGTDTDGVYYWEFRRNL---VR---DALALRSYLTPGDWVTGRSSSTDRKNGLSTEFFQGQNYTADHQQNPASTNDNTDQNLSTDVV Counts Percent NearbyLineage(s)
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 20502 1.74%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKSRNKAS___RYH__GY__KH___KY___HK______ 12333 1.05%
_I_---S_________D__Q_______---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 11223 0.95%
_I_---S__--_____D__________---G_---________________D_FPFANSN__RNKAV___RYH__GY__KH___KY___HK______ 9087 0.77%
_I_---S_________D__Q_______---E_---___________V____HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______ 8792 0.75%
_I_---S__--_____D__________---G_---________________D_FPFAN_NK_RNKAV___RYH__GY__KH___KY___HK______ 6526 0.56%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKAS___RYH__GY__KH___KY___HK______ 6012 0.51%
_I_---S_________D__________---G_---________________D_FPFANSNK_MNKR____RYH__GY__KH___KY___HK______ 4230 0.36%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 3887 0.33%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKSRNKAI___RYH__GY__KH___KY___HK______ 3597 0.31%
_I_---S_________D__Q_______---E_---____________G___HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______ 2778 0.24%
_I_---S__--_____D__________---G_---________________DTFPFANSN__RNKAV___RYH__GY__KH___KY___HK______ 2775 0.24%
_I_---S_________D___R_L____---G_---________________H_FPFANSNKS_NKA____RYH__GY__KH___KY___HK______ 2607 0.22%
_I_---S__--_____D__________---G_---________________D_FPFANSNK_RNKAV___RYH__G___KH___KY___HK______ 1963 0.17%
_I_---S__--________________---G_---________________D_FPFANSN__RNKAV___RYH__GY__KH___KY___HK______ 1929 0.16%
_I_---S__--_____D__________---G_---________________DTFPFAN_NK_RNKAV___RYH__GY__KH___KY___HK______ 1875 0.16%
_I_---S_________D__Q_______---E_---________________HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______ 1652 0.14%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKA____RYH__GY__KH___KY___HK______ 1526 0.13%
___---S__--_____D__________---G_---________________D_FPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 1486 0.13%
_I_---S__--_____D__________---G_---________________D_FPFAN_____NKAV___RYH__GY__KH___KY___HK______ 1169 0.10%
_________--_____D__________---G_---________________D_FPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 1158 0.10%
_I_---S__--_____D__________---G_---________________D_FPFANS_K_RNKAV___RYH__GY__KH___KY___HK______ 1128 0.10%
_I_---S__--_____D__________---G_---________________D_FPFANSNK_RNKAV___RYH__GY__K____KY___HK______ 1087 0.09%
_I_---S__--_____D__________---G_---________________DTFPFANS_K_RNKAV___RYH__GY__KH___KY___HK______ 1055 0.09%
_L_---S__--_____D__________---G_---________________D_FPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 899 0.08%
_I_---S__--________________---G_---________________DTFPFANSN__RNKAV___RYH__GY__KH___KY___HK______ 882 0.08%
_I_---S__--_____D_-________---G_---________________D_FPFANSNK_RNKAA___RYH__GY__KH___KY___HK______ 869 0.07%
_I_---S__--_____D__________---G_---________________D_FPFANSNK_RNKAV___RYH__GY__KH___K____HK______ 860 0.07%
_I_---S__--_____D__________---G_---________________D_FPFANSNK_RNKVV___RYH__GY__KH___KY___HK______ 668 0.06%
___---S__--_____D__________---G_---________________DTFPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 628 0.05%
_I_---S_________D___R_L____---G_---________________H_FPFANSNKSRNKA____RYH__GY__KH___KY___HK______ 625 0.05%
_I_---S__--_____D__________---E_---________________D_FPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 565 0.05%
_I_---S_________D___R_L____---G_---________________H_FPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 517 0.04%
_I_---S__--_____D__________---G_---________________D_FPFANSNK_RNKAI___RYH__GY__KH___KY___HK______ 500 0.04%
_I_---S_________D__________---G_---________________D_FPFANSNKSMNKRS___RYH__GY__KH___KY___HK______ 499 0.04%
_I_---S_________D__Q_______---E_---___________V____HTFPFANS_KS_NKASS__RYH__GY__KH___KY___HK______ 476 0.04%
_I_---S__--_____D__________---G_---________________DTFPFAN_____NKAV___RYH__GY__KH___KY___HK______ 473 0.04%
_I_---S_________D___R_L__G-----_---________________HTFPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 458 0.04%
_I_---S__--_____D__________---G_---________________DTFPFANSNK_RNKAV___RYH__GY__K____KY___HK______ 457 0.04%
_L_---S__--_____D__________---G_---________________DTFPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 433 0.04%
_I_---S__--_____D__________---G_---________________D_FPFA______NKAV___RYH__GY__KH___KY___HK______ 430 0.04%
_I_---S__--_____D_-________---G_---________________D_FPFAN_NK_RNKAV___RYH__GY__KH___KY___HK______ 428 0.04%
_I_---S_________D__________---G_---________________D_FPFAN_NK_RNKAV___RYH__GY__KH___KY___HK______ 428 0.04%
_I__S___________D_-__G--__S---__---HV_--_____________FPFANSNKSMNKAP___RYH__GY__KH___KY___HK______ 416 0.04%
_I_---S__--_____D__________---G_---________________DTFPFANSNK_RNRAV___RYH__GY__KH___KY___HK______ 390 0.03%
_I_---S_________D___R_L____---G_---________________HTFPFAN_NKS_NKA_S__RYH__GY__KH___KY___HK______ 378 0.03%
_I_---S__--_____D__________---G_---________________D_FPFANSNK_RNKAV___RYH__GY_______KY___HK______ 362 0.03%
_________--_____D__________---G_---________________DTFPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 360 0.03%
_I_---S__--_____D__________---G_---________________D_FPFANSNK_RNKAV___RY___GY__KH___KY___HK______ 349 0.03%
_I_---S__--_____D__________---G_---________________D__PFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 331 0.03%
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last modified: Sun Jan 22 23:40 2023
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Questions or comments? Contact us at seq-info@lanl.gov.
