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view test-data/test-constellations/definitions/cAY.4.json @ 0:5e8505f27681 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot commit 0bc6ed15054577af1089d55ef9aa1071d122eb6b
author iuc
date Tue, 08 Aug 2023 15:11:47 +0000
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{
    "label": "Delta (AY.4-like)",
    "description": "AY.4 lineage defining mutations",
    "sources": [
    ],
    "type": "variant",
    "variant": {
	"Pango_lineages": [
	    "AY.4"
	],
	"mrca_lineage": "AY.4",
        "lineage_name": "AY.4",
        "parent_lineage": "B.1.617.2",
        "incompatible_lineage_calls": [
            "AY.4.2"
        ],
	"representative_genome": ""
    },
    "tags": [
	"AY.4"
    ],
    "sites": [
        "del:28271:1",
        "del:22029:6",
        "del:28248:6",
        "orf1a:A1306S",
        "orf1a:P2046L",
        "orf1a:P2287S",
        "orf1a:A2529V",
        "nuc:C8986T",
        "orf1a:V2930L",
        "orf1a:T3255I",
        "orf1a:T3646A",
        "nuc:A11332G",
        "orf1b:P314L",
        "orf1b:G662S",
        "orf1b:P1000L",
        "orf1b:A1918V",
        "nuc:C27874T",
        "n:G215C",
        "nuc:G29742T"
    ],
    "intermediate": [
        "nuc:G210T:0.961862",
        "nuc:C241T:0.972018",
        "nuc:T17040C:0.468120",
        "spike:T95I:0.967111"
    ],
    "rules": {
        "min_alt": 12,
        "max_ref": 3,
        "orf1a:A2529V": "alt"
    }
}