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 6, 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...... 0 0.00% Omicron_BA.2+212SGR
.I.........................---G.---................D.FPFANSNK.RNKAV._.RYH..GY..KH...KY...HK...... 479 0.21% Omicron_BA.4andBA.5
.I..............D..........---G.---................D.FPFANSNK.QNKA..R.RYH..GY..KH.L.KY...HK...... 2 0.00% Omicron_BA.2+L452Q+S704L_BA.2.12.1
.I..__..........D..........---G.---................D.FPFANSNK._NKA..R.RYH..GY..KH...KY...HK...... 0 0.00% Omicron_BA.2+P25_,P26_
.I..--..........D..........---G.---................D.FPFANSN..MNKA..R.RYH..GY..KH...KY...HK...... 0 0.00% Omicron_BA.2+L452M
.I..............D..........---G.---................D.FPFANSTK..NKA..R.RYH..GY..KH...KY...HK...... 0 0.00% Omicron_BA.2+K417T
.I..--..........D..........---G.---................D.FPFANSN.._NKA..R.RYH..GY..KH...KY...HK...... 7 0.00% Omicron_BA.2
........V--...I............---..---................DKLPF.........A..R.RYH..GY..KH...KY...HK...... 1 0.00% Omicron_BA.1.1
........V--...I............---..---................D_.PF___..._..A..R.RYHK.GY..KH...KYK..HKF..... 0 0.00% Omicron_BA.1
........V--...I............---..EPE................D_.PF......_..A..R.RYH..GY..KH...KY...HK...... 1 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........ 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........ 1 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......._ 2 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.. 3 0.00% Alpha
The most common sequence patterns that are missed by the varint patterns
Missing: 3747 patterns, for a total of 230162 sequences
1111
1111111111222222222222222222222222223333334444444444444455556666667777788999990112
1122222266777893444455559111111111112444444455555893477770014457788999900471577780016955556882176
8904567979056058234526780122223444452234678901238999613565870627846036815704557911464669049127864
LTTLPPATAHVGTDTDGVYYWEFRRNL---VR---DALALRSYLTPGDWVTGRSSSTDRKNGLSTEFFQGQNYTADHQQNPASTNDNTDQNLSTDVV Counts Percent NearbyLineage(s)
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 94082 40.79%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______ 38061 16.50%
_I_---S_________D_-___L____---E_---___________V____HTFPFANSNKSRNKAPS__RYH__GY__KH___KY___HK______ 12582 5.45%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KHV__KY___HK______ 8950 3.88%
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 7840 3.40%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH_L_KY___HK______ 7412 3.21%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYHI_GY__KH___KY___HK______ 7104 3.08%
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______ 6974 3.02%
_I_---S_________D_-___L____---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 3493 1.51%
_I_---S__--_____D_-___SG_-I---G_---________________H_FPFANSNKSWNKKP___RYH_VGY__KR___KY___HK______ 3376 1.46%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKSRNKAS___RYH__GY__KH___KY___HK______ 3080 1.34%
_I__S___________D_-__G--__S---__---HV_--____________SFPFANSNKSRNKAP___RYH__GY__KH___KY___HK______ 1602 0.69%
_I_---S_________D___R_L____---G_---G_______________HTFPFANSNKSRNKAS___RYH__GY__KH___KY___HK______ 1318 0.57%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KHV__KY___HK______ 1225 0.53%
_I_---S_________D_-________---E_---___________V____HTFPFANS_KS_NKAPS__RYH__GY__KH___KY___HK______ 980 0.42%
_I_---S_________D_-________---E_---___________VG___HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 909 0.39%
_I_---S_________D_-________---E_---___________V____HTFPFAN_NKS_NKAPS__RYH__GY__KH___KY___HK______ 744 0.32%
_I__S___________D_-__G--__S---__---HV_--_____________FPFANSNKSMNKAP___RYH__GY__KH___KY___HK______ 703 0.30%
_I_---S_________D__________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 665 0.29%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 511 0.22%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPP__RYH__GY__KRV__KY___HK______ 500 0.22%
_I_---S_________D_-________---E_---___________V____HTFPFANS_KS_NRAPS__RYH__GY__KH___KY___HK______ 466 0.20%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NIAPS__RYH__GY__KH___KY___HK______ 462 0.20%
_I_---S_S_______D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KHV__KY___HK______ 423 0.18%
_I_---S_________D_-________---E_---_______H___V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 413 0.18%
_L_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 395 0.17%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKSQNRAPS__RYH__GY__KH___KY___HK______ 321 0.14%
___---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 315 0.14%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPP__RYH__GY__KH___KY___HK______ 303 0.13%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY_HKH___KY___HK______ 291 0.13%
_I_---S_________D__________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______ 279 0.12%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______ 272 0.12%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKSRNKAPS__RYH__GY__KH___KY___HK______ 250 0.11%
_I_---S_________D_-________---E_---H__________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 250 0.11%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GYK_KH___KY___HK______ 242 0.10%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK_____L 241 0.10%
_I_---S_________D_-________---E_---___________V____HTFPFAN_NKS_NRAPS__RYH__GY__KH___KY___HK______ 241 0.10%
_I_---S_________D_-________---E_---V__________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 235 0.10%
_I_---S_________D_-________---E_---_V__________G___HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 220 0.10%
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NNAPS__RYH__GY__KH___KY___HK______ 209 0.09%
_I_---S__--_____D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 193 0.08%
_I_---S_______I_D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 191 0.08%
_I_---S_________D_-________---E_---H__________V____HTFPFANSNKS_NRAPS__RYH__GY__KH_L_KY___HK______ 189 0.08%
_I_---S_____I___D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 187 0.08%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GYH_KH___KY___HK______ 183 0.08%
_I_---S____V____D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 182 0.08%
FR____________I_D_-_LG--___---G_---____________G___DTFPFANSNKDRNKAP___RYH__GY__KH___KY___HK______ 180 0.08%
_I_---S_________D_-_____S__---E_---____________G___HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______ 168 0.07%
_I_---S_________D_-________---E_---___________V____H_FPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 168 0.07%
_I_---S_________D_-________---D_---____________G___HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______ 166 0.07%
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last modified: Wed May 24 14:07 2023
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Questions or comments? Contact us at seq-info@lanl.gov.
Questions or comments? Contact us at seq-info@lanl.gov.
