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: May 28, 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...... 383817 56.38% Omicron_BA.4andBA.5
.I..............D..........---G.---................D.FPFANSNK.QNKA..R.RYH..GY..KH.L.KY...HK...... 10 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...... 4 0.00% Omicron_BA.2+L452M
.I..............D..........---G.---................D.FPFANSTK..NKA..R.RYH..GY..KH...KY...HK...... 5 0.00% Omicron_BA.2+K417T
.I..--..........D..........---G.---................D.FPFANSN.._NKA..R.RYH..GY..KH...KY...HK...... 55 0.01% Omicron_BA.2
........V--...I............---..---................DKLPF.........A..R.RYH..GY..KH...KY...HK...... 27 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...... 12 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........ 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......._ 0 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......._ 8 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. 1 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............... 0 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.. 0 0.00% Alpha
The most common sequence patterns that are missed by the varint patterns
Missing: 6530 patterns, for a total of 296814 sequences
1111
1111111111222222222222222222222222223333334444444444444455556666667777788999990112
1122222266777893444455559111111111112444444455555893477770014457788999900471577780016955556882176
8904567979056058234526780122223444452234678901238999613565870627846036815704557911464669049127864
LTTLPPATAHVGTDTDGVYYWEFRRNL---VR---DALALRSYLTPGDWVTGRSSSTDRKNGLSTEFFQGQNYTADHQQNPASTNDNTDQNLSTDVV Counts Percent NearbyLineage(s)
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 142339 20.91%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKSRNKAS___RYH__GY__KH___KY___HK______ 28338 4.16%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 27735 4.07%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 8374 1.23%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______ 8230 1.21%
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______ 5596 0.82%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYH__GY__KH___KY___HK______ 4758 0.70%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKSRNKAI___RYH__GY__KH___KY___HK______ 3765 0.55%
_I_---S_________D__________---G_---________________D_FPFANSNK_MNKR____RYH__GY__KH___KY___HK______ 2131 0.31%
_I_---S_________D_-________---E_---___________V____HTFPFANS_KS_NKAPS__RYH__GY__KH___KY___HK______ 2093 0.31%
_I_---S_________D_-________---E_---____________G___HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 2005 0.29%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NRAPS__RYHI_GY__KH___KY___HK______ 1606 0.24%
_I_---S__--_____D_-________---G_---________________D_FPFANSNK_RNKAA___RYH__GY__KH___KY___HK______ 1222 0.18%
_I_---S_________D_-________---E_---________________HTFPFANSNKS_NKASS__RYH__GY__KH___KY___HK______ 1077 0.16%
_I_---S__--_____D__________---G_---________________DTFPFANS_K_RNKAV___RYH__GY__KH___KY___HK______ 1055 0.15%
_I_---S_________D_-________---E_---___________V____HTFPFAN_NKS_NKAPS__RYH__GY__KH___KY___HK______ 1051 0.15%
_I_---S__--_____D__________---G_---________________DTFPFAN_NK_RNKAV___RYH__GY__KH___KY___HK______ 1023 0.15%
_I_---S__--_____D__________---G_---________________DTFPFANSN__RNKAV___RYH__GY__KH___KY___HK______ 935 0.14%
_I_---S_________D_-________---E_---________________HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 919 0.13%
_I_---S_________D_-________---E_---___________V____HTFPFAN_NKS__KAPS__RYH__GY__KH___KY___HK______ 795 0.12%
_I_---S_________D__________---G_---________________D_FPFANSNKSMNKRS___RYH__GY__KH___KY___HK______ 733 0.11%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKAS___RYH__GY__KH___KY___HK______ 705 0.10%
_I_---S_________D___R_L____---G_---G_______________HTFPFANSNKSRNKAS___RYH__GY__KH___KY___HK______ 656 0.10%
_I_---S_________D___R_L____---G_---________________H_FPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 593 0.09%
_I_---S_________D_-________---E_---___________V____HTFPFANS_KS_NKASS__RYH__GY__KH___KY___HK______ 586 0.09%
_I_---S_________D_-________---E_---H__________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 573 0.08%
_I_---S__--_____D_-________---G_---________________DTFPFANS_K_RNKAV___RYH__GY__KH___KY___HK______ 572 0.08%
_I_---S__--_____D__________---G_---________________DTFPFANSNK_RNRAV___RYH__GY__KH___KY___HK______ 560 0.08%
_I_---S__--_____D__________---G_---________________D_FPFAN_NK_RNKAV___RYH__GY__KH___KY___HK______ 540 0.08%
_I_---S_________D__________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 537 0.08%
_I_---S_________D___R_L__G-----_---________________HTFPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 525 0.08%
_I__S___________D_-__G--__S---__---HV_--_____________FPFANSNKSMNKAP___RYH__GY__KH___KY___HK______ 521 0.08%
_I__S___________D_-__G--__S---__---HV_--____________SFPFANSNKSRNKAP___RYH__GY__KH___KY___HK______ 520 0.08%
_I_---S__--_____D__________---G_---________________D_FPFANS_K_RNKAV___RYH__GY__KH___KY___HK______ 513 0.08%
_I_---S__--_____D_-________---G_---________________DTFPFAN_NK_RNKAV___RYH__GY__KH___KY___HK______ 505 0.07%
_I_---S__--________________---G_---________________DTFPFANSN__RNKAV___RYH__GY__KH___KY___HK______ 489 0.07%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KHV__KY___HK______ 459 0.07%
_I_---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GYH_KH___KY___HK______ 441 0.06%
_I_---S_________D__HR_L____---G_---________________HTFPFANSNKS_NKA_S__RYH__GY__KH___KY___HK______ 428 0.06%
_I_---S_________D___R_L____---G_---________________H_FPFANSNKSRNKA____RYH__GY__KH___KY___HK______ 395 0.06%
_I_---S_________D___R_L____---G_---________________HTFPFANSNKS_NKA____RYH__GY__KH___KY___HK______ 376 0.06%
_I_---S_________D___R_L____---G_---________________HTFPFAN_NKS_NKA_S__RYH__GY__KH___KY___HK______ 369 0.05%
_I_---S__--_____D__________---G_---________________D_FPFANSN__RNKAV___RYH__GY__KH___KY___HK______ 368 0.05%
___---S__--_____D__________---G_---________________DTFPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 365 0.05%
_I_---S___________-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 355 0.05%
_L_---S__--_____D__________---G_---________________DTFPFANSNK_RNKAV___RYH__GY__KH___KY___HK______ 351 0.05%
_I_---S___________-________---E_---___________V____HTFPFANS_KS_NKAPS__RYH__GY__KH___KY___HK______ 320 0.05%
___---S_________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 317 0.05%
_I_---S_________D_-________---EL---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 273 0.04%
_I_---SI________D_-________---E_---___________V____HTFPFANSNKS_NKAPS__RYH__GY__KH___KY___HK______ 271 0.04%
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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.
