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bf42tree.json
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{ "version": "v2", "meta": { "title": "Subtree with Japan\/PG-462868\/2023|EPI_ISL_17243060|2023-02-28 and 51 other uploaded samples", "description": "Dataset generated by [UShER web interface](https:\/\/genome.ucsc.edu\/cgi-bin\/hgPhyloPlace) using the [usher](https:\/\/github.com\/yatisht\/usher\/) program. If you have metadata you wish to display, you can now drag on a CSV file and it will be added into this view, [see here](https:\/\/docs.nextstrain.org\/projects\/auspice\/en\/latest\/advanced-functionality\/drag-drop-csv-tsv.html) for more info.", "panels": [ "tree", "entropy"] , "display_defaults": { "branch_label": "aa mutations", "color_by": "pango_lineage_usher"} , "colorings": [ { "key": "userOrOld", "title": "Sample type", "type": "categorical", "scale": [ [ "uploaded sample", "#CC0000"] , [ "GISAID and\/or public", "#000000"] ] } , { "key": "gt", "title": "Genotype", "type": "categorical"} , { "key": "pango_lineage", "title": "Pango lineage", "type": "categorical"} , { "key": "Nextstrain_clade", "title": "Nextstrain Clade", "type": "categorical", "scale": [ [ "20H (Beta, V2)", "#5E1D9D"] , [ "20I (Alpha, V1)", "#492AB5"] , [ "20J (Gamma, V3)", "#4042C7"] , [ "21A (Delta)", "#3E5DD0"] , [ "21I (Delta)", "#4377CD"] , [ "21J (Delta)", "#4A8CC2"] , [ "21B (Kappa)", "#549DB2"] , [ "21C (Epsilon)", "#60AA9E"] , [ "21D (Eta)", "#6EB389"] , [ "21E (Theta)", "#80B974"] , [ "21F (Iota)", "#92BC63"] , [ "21G (Lambda)", "#A6BE55"] , [ "21H (Mu)", "#B9BC4A"] , [ "21K (Omicron)", "#CBB742"] , [ "21L (Omicron)", "#D9AD3D"] , [ "21M (Omicron)", "#E29D39"] , [ "22A (Omicron)", "#E68634"] , [ "22B (Omicron)", "#E56A2F"] , [ "22C (Omicron)", "#E04929"] , [ "22D (Omicron)", "#DB2823"] , [ "uploaded sample", "#000000"] ] } , { "key": "pango_lineage_usher", "title": "Pango lineage assigned by UShER", "type": "categorical"} , { "key": "Nextstrain_clade_usher", "title": "Nextstrain Clade assigned by UShER", "type": "categorical", "scale": [ [ "20H (Beta, V2)", "#5E1D9D"] , [ "20I (Alpha, V1)", "#492AB5"] , [ "20J (Gamma, V3)", "#4042C7"] , [ "21A (Delta)", "#3E5DD0"] , [ "21I (Delta)", "#4377CD"] , [ "21J (Delta)", "#4A8CC2"] , [ "21B (Kappa)", "#549DB2"] , [ "21C (Epsilon)", "#60AA9E"] , [ "21D (Eta)", "#6EB389"] , [ "21E (Theta)", "#80B974"] , [ "21F (Iota)", "#92BC63"] , [ "21G (Lambda)", "#A6BE55"] , [ "21H (Mu)", "#B9BC4A"] , [ "21K (Omicron)", "#CBB742"] , [ "21L (Omicron)", "#D9AD3D"] , [ "21M (Omicron)", "#E29D39"] , [ "22A (Omicron)", "#E68634"] , [ "22B (Omicron)", "#E56A2F"] , [ "22C (Omicron)", "#E04929"] , [ "22D (Omicron)", "#DB2823"] , [ "uploaded sample", "#000000"] ] } , { "key": "country", "title": "Country", "type": "categorical"} ] , "filters": [ "userOrOld", "country", "pango_lineage_usher", "pango_lineage", "Nextstrain_clade_usher", "Nextstrain_clade"] , "genome_annotations": { "ORF1ab": { "start": 266, "end": 21555, "strand": "+", "type": "CDS"} , "S": { "start": 21563, "end": 25384, "strand": "+", "type": "CDS"} , "ORF3a": { "start": 25393, "end": 26220, "strand": "+", "type": "CDS"} , "E": { "start": 26245, "end": 26472, "strand": "+", "type": "CDS"} , "M": { "start": 26523, "end": 27191, "strand": "+", "type": "CDS"} , "ORF6": { "start": 27202, "end": 27387, "strand": "+", "type": "CDS"} , "ORF7a": { "start": 27394, "end": 27759, "strand": "+", "type": "CDS"} , "ORF7b": { "start": 27756, "end": 27887, "strand": "+", "type": "CDS"} , "ORF8": { "start": 27894, "end": 28259, "strand": "+", "type": "CDS"} , "N": { "start": 28274, "end": 29533, "strand": "+", "type": "CDS"} , "ORF10": { "start": 29558, "end": 29674, "strand": "+", "type": "CDS"} , "nuc": { "start": 1, "end": 29903, "strand": "+", "type": "source"} } } , "tree": { "name": "wrapper", "children": [ { "name": "node_7903711", "branch_attrs": { "labels": { "id": "node_7903711", "nuc mutations": "C241T,T670G,C1627T,C2790T,C3037T,G4184A,C4321T,C9344T,A9424G,C9534T,C10029T,C10198T,G10447A,C10449A,G12160A,C12880T,C14408T,C15714T,C17410T,A18163G,C19955T,A20055G,C21618T,T22200G,G22578A,C22674T,T22679C,C22686T,A22688G,G22775A,A22786C,G22813T,T22882G,T22917G,G22992A,C22995A,A23013C,T23018G,A23055G,A23063T,T23075C,A23403G,C23525T,T23599G,C23604A,C23854A,G23948T,A24424T,T24469A,C25000T,C25584T,C26060T,C26270T,G26529A,C26577G,G26709A,A27038G,C27807T,C27889T,A28271T,C28311T,A28330G,G28881A,G28882A,G28883C,A29510C", "back-mutations": "", "aa mutations": "ORF1ab:S135R,ORF1ab:T842I,ORF1ab:G1307S,ORF1ab:L3027F,ORF1ab:T3090I,ORF1ab:T3255I,ORF1ab:P3395H,ORF1ab:P4715L,ORF1ab:R5716C,ORF1ab:I5967V,ORF1ab:T6564I,S:T19I,S:V213G,S:G339D,S:S371F,S:S373P,S:S375F,S:T376A,S:D405N,S:R408S,S:K417N,S:N440K,S:L452R,S:S477N,S:T478K,S:E484A,S:F486V,S:Q498R,S:N501Y,S:Y505H,S:D614G,S:H655Y,S:N679K,S:P681H,S:N764K,S:D796Y,S:Q954H,S:N969K,ORF3a:T223I,E:T9I,M:D3N,M:Q19E,M:A63T,N:P13L,N:R203K,N:G204R,N:S413R", "Spike mutations": "S:T19I,S:V213G,S:G339D,S:S371F,S:S373P,S:S375F,S:T376A,S:D405N,S:R408S,S:K417N,S:N440K,S:L452R,S:S477N,S:T478K,S:E484A,S:F486V,S:Q498R,S:N501Y,S:Y505H,S:D614G,S:H655Y,S:N679K,S:P681H,S:N764K,S:D796Y,S:Q954H,S:N969K"} , "mutations": { "ORF1ab": [ "S135R", "T842I", "G1307S", "L3027F", "T3090I", "T3255I", "P3395H", "P4715L", "R5716C", "I5967V", "T6564I"] , "S": [ "T19I", "V213G", "G339D", "S371F", "S373P", "S375F", "T376A", "D405N", "R408S", "K417N", "N440K", "L452R", "S477N", "T478K", "E484A", "F486V", "Q498R", "N501Y", "Y505H", "D614G", "H655Y", "N679K", "P681H", "N764K", "D796Y", "Q954H", "N969K"] , "ORF3a": [ "T223I"] , "E": [ "T9I"] , "M": [ "D3N", "Q19E", "A63T"] , "N": [ "P13L", "R203K", "G204R", "S413R"] , "nuc": [ "C241T", "T670G", "C1627T", "C2790T", "C3037T", "G4184A", "C4321T", "C9344T", "A9424G", "C9534T", "C10029T", "C10198T", "G10447A", "C10449A", "G12160A", "C12880T", "C14408T", "C15714T", "C17410T", "A18163G", "C19955T", "A20055G", "C21618T", "T22200G", "G22578A", "C22674T", "T22679C", "C22686T", "A22688G", "G22775A", "A22786C", "G22813T", "T22882G", "T22917G", "G22992A", "C22995A", "A23013C", "T23018G", "A23055G", "A23063T", "T23075C", "A23403G", "C23525T", "T23599G", "C23604A", "C23854A", "G23948T", "A24424T", "T24469A", "C25000T", "C25584T", "C26060T", "C26270T", "G26529A", "C26577G", "G26709A", "A27038G", "C27807T", "C27889T", "A28271T", "C28311T", "A28330G", "G28881A", "G28882A", "G28883C", "A29510C"] } } , "children": [ { "name": "Qatar\/QA.QU_20.28.G6\/2022|EPI_ISL_16076709|2022-07-08", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-07-08"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Qatar"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "USA\/CA-SEARCH-208868\/2022|EPI_ISL_16102486|2022-09-23", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-09-23"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "USA"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Brazil\/SP-FIOCRUZ-125009CE\/2022|EPI_ISL_15965090|2022-07-08", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-07-08"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Brazil"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Brazil\/RJ-COVID-19_UFRJ-68912\/2022|EPI_ISL_16083780|2022-10-06", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-10-06"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "Unassigned", "url": "https:\/\/outbreak.info\/situation-reports?pango=Unassigned"} , "genbank_accession": { "value": ""} , "country": { "value": "Brazil"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Brazil\/GO-LACENGO-520340411\/2022|EPI_ISL_16112063|2022-06-20", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-06-20"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Brazil"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Brazil\/GO-LACENGO-520340533\/2022|EPI_ISL_16112112|2022-06-28", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-06-28"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Brazil"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Japan\/PG-406756\/2022|EPI_ISL_16107647|2022-12-05", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-12-05"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Japan"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Japan\/PG-406754\/2022|EPI_ISL_16107645|2022-12-05", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-12-05"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Japan"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Germany\/RP-RKI-I-1054954\/2022|EPI_ISL_16148267|2022-10-17", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-10-17"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "Unassigned", "url": "https:\/\/outbreak.info\/situation-reports?pango=Unassigned"} , "genbank_accession": { "value": ""} , "country": { "value": "Germany"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Germany\/NI-RKI-I-1058580\/2022|EPI_ISL_16152146|2022-11-21", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-11-21"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Germany"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Germany\/BW-RKI-I-1060237\/2022|EPI_ISL_16153840|2022-11-12", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-11-12"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "Unassigned", "url": "https:\/\/outbreak.info\/situation-reports?pango=Unassigned"} , "genbank_accession": { "value": ""} , "country": { "value": "Germany"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Germany\/NI-RKI-I-1058554\/2022|EPI_ISL_16152120|2022-11-22", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-11-22"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Germany"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "USA\/NMDOH-2022118274\/2022|OQ368776.1|2022-07-19", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-07-19"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": "OQ368776.1"} , "country": { "value": "USA"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Slovenia\/224108\/2022|EPI_ISL_15387787|2022-09-14", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-09-14"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Slovenia"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "USA\/NMDOH-2022107891\/2022|OQ095446.1|2022-07-08", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-07-08"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": "OQ095446.1"} , "country": { "value": "USA"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Brazil\/AM-FIOCRUZ-ILMD2206203\/2022|EPI_ISL_16230099|2022-08-07", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-08-07"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Brazil"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Japan\/RIMD15774\/2022|EPI_ISL_16242016|2022-07-28", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-07-28"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Japan"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} } } , { "name": "Peru\/CUS-INS-35298\/2022|EPI_ISL_16207761|2022-07-13", "node_attrs": { "div": 66, "userOrOld": { "value": "GISAID and\/or public"} , "date": { "value": "2022-07-13"} , "Nextstrain_clade": { "value": "22B"} , "pango_lineage": { "value": "BA.5.2.1", "url": "https:\/\/outbreak.info\/situation-reports?pango=BA.5.2.1"} , "genbank_accession": { "value": ""} , "country": { "value": "Peru"} , "Nextstrain_clade_usher": { "value": "22B (Omicron)"} , "pango_lineage_usher": { "value": 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