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subtreeAuspice_genome_10868_1eeed0.json
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subtreeAuspice_genome_10868_1eeed0.json
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{
"version": "v2",
"meta": {
"title": "Subtree with XBB.1.5 + S:Q613H 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)", "#5E1D9D" ],
[ "20I (Alpha)", "#4D22AD" ],
[ "20J (Gamma)", "#4530BB" ],
[ "21A (Delta)", "#403FC6" ],
[ "21J (Delta)", "#3F51CC" ],
[ "21K (Delta)", "#3F62D0" ],
[ "21B (Kappa)", "#4272CE" ],
[ "21C (Epsilon)", "#4681CA" ],
[ "21D (Eta)", "#4B8EC2" ],
[ "21E (Theta)", "#5199B8" ],
[ "21F (Iota)", "#58A2AC" ],
[ "21G (Lambda)", "#60AA9F" ],
[ "21H (Mu)", "#69B091" ],
[ "21K (BA.1)", "#72B584" ],
[ "21L (BA.2)", "#7DB877" ],
[ "21M (Omicron)", "#89BB6B" ],
[ "22A (BA.4)", "#95BD61" ],
[ "22B (BA.5)", "#A1BE58" ],
[ "22C (BA.2.12.1)", "#AEBD50" ],
[ "22D (BA.2.75)", "#BABC4A" ],
[ "22E (BQ.1)", "#C5B945" ],
[ "22F (XBB)", "#D0B441" ],
[ "23A (XBB.1.5)", "#D8AE3E" ],
[ "23B (XBB.1.16)", "#DFA43B" ],
[ "23C (CH.1.1)", "#E49938" ],
[ "23D (XBB.1.9)", "#E68B35" ],
[ "23E (XBB.2.3)", "#E67A32" ],
[ "23F (EG.5.1)", "#E4672E" ],
[ "23G (XBB.1.5.70)", "#E1522A" ],
[ "23H (HK.3)", "#DE3D27" ],
[ "23I (BA.2.86)", "#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)", "#5E1D9D" ],
[ "20I (Alpha)", "#4D22AD" ],
[ "20J (Gamma)", "#4530BB" ],
[ "21A (Delta)", "#403FC6" ],
[ "21J (Delta)", "#3F51CC" ],
[ "21K (Delta)", "#3F62D0" ],
[ "21B (Kappa)", "#4272CE" ],
[ "21C (Epsilon)", "#4681CA" ],
[ "21D (Eta)", "#4B8EC2" ],
[ "21E (Theta)", "#5199B8" ],
[ "21F (Iota)", "#58A2AC" ],
[ "21G (Lambda)", "#60AA9F" ],
[ "21H (Mu)", "#69B091" ],
[ "21K (BA.1)", "#72B584" ],
[ "21L (BA.2)", "#7DB877" ],
[ "21M (Omicron)", "#89BB6B" ],
[ "22A (BA.4)", "#95BD61" ],
[ "22B (BA.5)", "#A1BE58" ],
[ "22C (BA.2.12.1)", "#AEBD50" ],
[ "22D (BA.2.75)", "#BABC4A" ],
[ "22E (BQ.1)", "#C5B945" ],
[ "22F (XBB)", "#D0B441" ],
[ "23A (XBB.1.5)", "#D8AE3E" ],
[ "23B (XBB.1.16)", "#DFA43B" ],
[ "23C (CH.1.1)", "#E49938" ],
[ "23D (XBB.1.9)", "#E68B35" ],
[ "23E (XBB.2.3)", "#E67A32" ],
[ "23F (EG.5.1)", "#E4672E" ],
[ "23G (XBB.1.5.70)", "#E1522A" ],
[ "23H (HK.3)", "#DE3D27" ],
[ "23I (BA.2.86)", "#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_6880832",
"branch_attrs": {
"labels": {
"id": "node_6880832",
"aa mutations": "ORF1ab:K47R,ORF1ab:S135R,ORF1ab:T842I,ORF1ab:G1307S,ORF1ab:L3027F,ORF1ab:T3090I,ORF1ab:L3201F,ORF1ab:T3255I,ORF1ab:M3280V,ORF1ab:P3395H,ORF1ab:P4715L,ORF1ab:G5063S,ORF1ab:S5360P,ORF1ab:R5716C,ORF1ab:I5967V,ORF1ab:T6564I,S:T19I,S:V83A,S:H146Q,S:Q183E,S:V213E,S:G252V,S:G339H,S:R346T,S:L368I,S:S371F,S:S373P,S:S375F,S:T376A,S:D405N,S:R408S,S:K417N,S:N440K,S:V445P,S:G446S,S:N460K,S:S477N,S:T478K,S:E484A,S:F486P,S:F490S,S:Q498R,S:N501Y,S:Y505H,S:Q613H,S:D614G,S:H655Y,S:N679K,S:P681H,S:N764K,S:D796Y,S:Q954H,S:N969K,S:H1058Y,ORF3a:T223I,E:T9I,E:T11A,M:Q19E,M:A63T,ORF6:D61L,ORF8:G8*,N:P13L,N:R203K,N:G204R,N:S413R",
"back-mutations": "",
"nuc mutations": "C241T,A405G,T670G,C2790T,C3037T,G4184A,C4321T,C4993T,C9344T,A9424G,C9534T,C9866T,C10029T,A10103G,C10198T,T10204C,G10447A,C10449A,C12025T,C12880T,C14408T,G15451A,C15714T,C15738T,T15939C,T16342C,T17124C,C17410T,T17859C,A18163G,A19326G,C19955T,A20055G,C21618T,T21810C,C22000A,C22109G,T22200A,G22317T,G22577C,G22578A,G22599C,C22664A,C22674T,T22679C,C22686T,A22688G,G22775A,A22786C,G22813T,T22882G,G22895C,T22896C,G22898A,T22942G,G22992A,C22995A,A23013C,T23018C,T23019C,T23031C,A23055G,A23063T,T23075C,G23401T,A23403G,T23488C,C23525T,T23599G,C23604A,C23854A,G23948T,A24424T,T24469A,C24734T,C25000T,C25416T,C25584T,C26060T,C26270T,A26275G,C26577G,G26709A,C26858T,A27259C,G27382C,A27383T,T27384C,C27807T,G27915T,A28271T,C28311T,G28881A,G28882A,G28883C,A29510C,G29543T",
"Spike mutations": "S:T19I,S:V83A,S:H146Q,S:Q183E,S:V213E,S:G252V,S:G339H,S:R346T,S:L368I,S:S371F,S:S373P,S:S375F,S:T376A,S:D405N,S:R408S,S:K417N,S:N440K,S:V445P,S:G446S,S:N460K,S:S477N,S:T478K,S:E484A,S:F486P,S:F490S,S:Q498R,S:N501Y,S:Y505H,S:Q613H,S:D614G,S:H655Y,S:N679K,S:P681H,S:N764K,S:D796Y,S:Q954H,S:N969K,S:H1058Y"
},
"mutations": {
"ORF1ab": [ "K47R", "S135R", "T842I", "G1307S", "L3027F", "T3090I", "L3201F", "T3255I", "M3280V", "P3395H", "P4715L", "G5063S", "S5360P", "R5716C", "I5967V", "T6564I" ],
"S": [ "T19I", "V83A", "H146Q", "Q183E", "V213E", "G252V", "G339H", "R346T", "L368I", "S371F", "S373P", "S375F", "T376A", "D405N", "R408S", "K417N", "N440K", "V445P", "G446S", "N460K", "S477N", "T478K", "E484A", "F486P", "F490S", "Q498R", "N501Y", "Y505H", "Q613H", "D614G", "H655Y", "N679K", "P681H", "N764K", "D796Y", "Q954H", "N969K", "H1058Y" ],
"ORF3a": [ "T223I" ],
"E": [ "T9I", "T11A" ],
"M": [ "Q19E", "A63T" ],
"ORF6": [ "D61L" ],
"ORF8": [ "G8*" ],
"N": [ "P13L", "R203K", "G204R", "S413R" ],
"nuc": [ "C241T", "A405G", "T670G", "C2790T", "C3037T", "G4184A", "C4321T", "C4993T", "C9344T", "A9424G", "C9534T", "C9866T", "C10029T", "A10103G", "C10198T", "T10204C", "G10447A", "C10449A", "C12025T", "C12880T", "C14408T", "G15451A", "C15714T", "C15738T", "T15939C", "T16342C", "T17124C", "C17410T", "T17859C", "A18163G", "A19326G", "C19955T", "A20055G", "C21618T", "T21810C", "C22000A", "C22109G", "T22200A", "G22317T", "G22577C", "G22578A", "G22599C", "C22664A", "C22674T", "T22679C", "C22686T", "A22688G", "G22775A", "A22786C", "G22813T", "T22882G", "G22895C", "T22896C", "G22898A", "T22942G", "G22992A", "C22995A", "A23013C", "T23018C", "T23019C", "T23031C", "A23055G", "A23063T", "T23075C", "G23401T", "A23403G", "T23488C", "C23525T", "T23599G", "C23604A", "C23854A", "G23948T", "A24424T", "T24469A", "C24734T", "C25000T", "C25416T", "C25584T", "C26060T", "C26270T", "A26275G", "C26577G", "G26709A", "C26858T", "A27259C", "G27382C", "A27383T", "T27384C", "C27807T", "G27915T", "A28271T", "C28311T", "G28881A", "G28882A", "G28883C", "A29510C", "G29543T" ]
}
},
"children": [
{
"name": "USA\/TX-CDC-QDX47145199\/2023|EPI_ISL_17180122|2023-02-22",
"branch_attrs": {
"mutations": {
"ORF1ab": [ "T4355I" ],
"nuc": [ "C13329T" ]
}
},
"node_attrs": {
"div": 98,
"userOrOld": { "value": "uploaded sample" },
"Nextstrain_clade": { "value": "uploaded sample" },
"GISAID_clade": { "value": "uploaded sample" },
"pango_lineage": {
"value": "uploaded sample",
"url": "uploaded sample"
},
"Nextstrain_lineage": { "value": "uploaded sample" },
"country": { "value": "USA" },
"Nextstrain_clade_usher": { "value": "23A (XBB.1.5)" },
"pango_lineage_usher": {
"value": "XBB.1.5",
"url": "https:\/\/outbreak.info\/situation-reports?pango=XBB.1.5"
},
"subtree": {
"value": "view subtree 6",
"url": "https:\/\/nextstrain.org\/fetch\/genome.ucsc.edu\/cgi-bin\/..\/trash\/ct\/subtreeAuspice6_genome_10868_1eeed0.json?f_userOrOld=uploaded%20sample"
}
}
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