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subtreeAuspice_genome_664cc_695f20.json
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subtreeAuspice_genome_664cc_695f20.json
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{
"version": "v2",
"meta": {
"title": "Subtree with XDQ samples",
"description": "Dataset generated by [UShER web interface](https:\/\/genome-test.gi.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" ],
[ "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": [
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[ "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": [
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[ "20I (Alpha)", "#4D22AD" ],
[ "20J (Gamma)", "#4530BB" ],
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[ "21B (Kappa)", "#4272CE" ],
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[ "22B (BA.5)", "#A1BE58" ],
[ "22C (BA.2.12.1)", "#AEBD50" ],
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[ "22F (XBB)", "#D0B441" ],
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[ "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": {
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},
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}
],
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"strand": "+",
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},
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"end": 26220,
"strand": "+",
"type": "CDS"
},
"E": {
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"end": 26472,
"strand": "+",
"type": "CDS"
},
"M": {
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"end": 27191,
"strand": "+",
"type": "CDS"
},
"ORF6": {
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"end": 27387,
"strand": "+",
"type": "CDS"
},
"ORF7a": {
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"end": 27759,
"strand": "+",
"type": "CDS"
},
"ORF7b": {
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"end": 27887,
"strand": "+",
"type": "CDS"
},
"ORF8": {
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"end": 28259,
"strand": "+",
"type": "CDS"
},
"N": {
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"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_6829602",
"branch_attrs": {
"labels": {
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"nuc mutations": "C241T,T670G,C897A,C2790T,C3037T,G3431T,G4184A,C4321T,A6183G,C7420T,A7842G,C8293T,G8393A,C9344T,A9424G,C9534T,C10029T,C10198T,G10447A,C10449A,G11042T,C12789T,C12815T,C12880T,T13339C,C14408T,C15714T,T15756A,C17410T,A18163G,A18492G,C19955T,A20055G,C21618T,C21622T,G21624C,C21711T,G21941T,T22032C,C22033A,A22034G,T22200G,C22208T,C22295A,C22353A,A22556G,G22577C,G22578A,A22629C,C22674T,T22679C,C22686T,A22688G,G22770A,G22775A,A22786C,G22813T,T22882G,G22895C,T22896A,G22898A,A22910G,C22916T,T22917G,T22942A,G22992A,C22995A,T23005A,G23012A,T23018C,T23019C,A23055G,A23063T,T23075C,G23222A,C23271T,A23403G,C23423T,C23525T,T23599G,C23604G,C23854A,G23948T,A24424T,T24469A,C25000T,C25416T,C25584T,C26060T,C26270T,A26275G,C26577G,G26709A,C26858T,A27259C,G27382C,A27383T,T27384C,C27807T,G27915T,A27980G,A28271T,T28297C,C28311T,C28846T,G28881A,G28882A,G28883C,T29023C,A29510C",
"back-mutations": "",
"aa mutations": "ORF1ab:S135R,ORF1ab:A211D,ORF1ab:T842I,ORF1ab:V1056L,ORF1ab:G1307S,ORF1ab:K1973R,ORF1ab:N2526S,ORF1ab:A2710T,ORF1ab:L3027F,ORF1ab:T3090I,ORF1ab:T3255I,ORF1ab:P3395H,ORF1ab:V3593F,ORF1ab:T4175I,ORF1ab:P4715L,ORF1ab:R5716C,ORF1ab:I5967V,ORF1ab:T6564I,S:T19I,S:R21T,S:S50L,S:V127F,S:F157S,S:R158G,S:V213G,S:L216F,S:H245N,S:A264D,S:I332V,S:G339H,S:K356T,S:S371F,S:S373P,S:S375F,S:T376A,S:R403K,S:D405N,S:R408S,S:K417N,S:N440K,S:V445H,S:G446S,S:N450D,S:L452W,S:N460K,S:S477N,S:T478K,S:N481K,S:E484K,S:F486P,S:Q498R,S:N501Y,S:Y505H,S:E554K,S:A570V,S:D614G,S:P621S,S:H655Y,S:N679K,S:P681R,S:N764K,S:D796Y,S:S939F,S:Q954H,S:N969K,S:P1143L,ORF3a:T223I,E:T9I,E:T11A,M:Q19E,M:A63T,ORF6:D61L,ORF8:G8*,N:P13L,N:R203K,N:G204R,N:S413R",
"Spike mutations": "S:T19I,S:R21T,S:S50L,S:V127F,S:F157S,S:R158G,S:V213G,S:L216F,S:H245N,S:A264D,S:I332V,S:G339H,S:K356T,S:S371F,S:S373P,S:S375F,S:T376A,S:R403K,S:D405N,S:R408S,S:K417N,S:N440K,S:V445H,S:G446S,S:N450D,S:L452W,S:N460K,S:S477N,S:T478K,S:N481K,S:E484K,S:F486P,S:Q498R,S:N501Y,S:Y505H,S:E554K,S:A570V,S:D614G,S:P621S,S:H655Y,S:N679K,S:P681R,S:N764K,S:D796Y,S:S939F,S:Q954H,S:N969K,S:P1143L"
},
"mutations": {
"ORF1ab": [ "S135R", "A211D", "T842I", "V1056L", "G1307S", "K1973R", "N2526S", "A2710T", "L3027F", "T3090I", "T3255I", "P3395H", "V3593F", "T4175I", "P4715L", "R5716C", "I5967V", "T6564I" ],
"S": [ "T19I", "R21T", "S50L", "V127F", "F157S", "R158G", "V213G", "L216F", "H245N", "A264D", "I332V", "G339H", "K356T", "S371F", "S373P", "S375F", "T376A", "R403K", "D405N", "R408S", "K417N", "N440K", "V445H", "G446S", "N450D", "L452W", "N460K", "S477N", "T478K", "N481K", "E484K", "F486P", "Q498R", "N501Y", "Y505H", "E554K", "A570V", "D614G", "P621S", "H655Y", "N679K", "P681R", "N764K", "D796Y", "Q954H", "N969K" ],
"ORF3a": [ "T223I" ],
"E": [ "T9I", "T11A" ],
"M": [ "Q19E", "A63T" ],
"ORF6": [ "D61L" ],
"ORF8": [ "G8*" ],
"N": [ "P13L", "R203K", "G204R", "S413R" ],
"nuc": [ "C241T", "T670G", "C897A", "C2790T", "C3037T", "G3431T", "G4184A", "C4321T", "A6183G", "C7420T", "A7842G", "C8293T", "G8393A", "C9344T", "A9424G", "C9534T", "C10029T", "C10198T", "G10447A", "C10449A", "G11042T", "C12789T", "C12815T", "C12880T", "T13339C", "C14408T", "C15714T", "T15756A", "C17410T", "A18163G", "A18492G", "C19955T", "A20055G", "C21618T", "C21622T", "G21624C", "C21711T", "G21941T", "T22032C", "C22033A", "A22034G", "T22200G", "C22208T", "C22295A", "C22353A", "A22556G", "G22577C", "G22578A", "A22629C", "C22674T", "T22679C", "C22686T", "A22688G", "G22770A", "G22775A", "A22786C", "G22813T", "T22882G", "G22895C", "T22896A", "G22898A", "A22910G", "C22916T", "T22917G", "T22942A", "G22992A", "C22995A", "T23005A", "G23012A", "T23018C", "T23019C", "A23055G", "A23063T", "T23075C", "G23222A", "C23271T", "A23403G", "C23423T", "C23525T", "T23599G", "C23604G", "C23854A", "G23948T", "A24424T", "T24469A", "C25000T", "C25416T", "C25584T", "C26060T", "C26270T", "A26275G", "C26577G", "G26709A", "C26858T", "A27259C", "G27382C", "A27383T", "T27384C", "C27807T", "G27915T", "A27980G", "A28271T", "T28297C", "C28311T", "C28846T", "G28881A", "G28882A", "G28883C", "T29023C", "A29510C" ]
}
},
"children": [
{
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