reference allele [GENO_0000036]

An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome. Being a ‘reference allele’ is a role or status assigned in the context of a specific dataset or analysis. In human variation datasets, ‘reference’ status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene. For example, ‘reference alleles’ in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population. In model organism datasets, ‘reference’ alleles are typically (but not always) the ‘wild-type’ variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared.
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Open reference allele in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/GENO_0000036",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000036",
            "label": "reference allele"
        },
        "description": [
            "An allele whose sequence matches what is consdiered to be the reference sequence at that location in the genome."
        ],
        "comment": [
            "Being a 'reference allele' is a role or status assigned in the context of a specific dataset or analysis.  In human variation datasets, 'reference' status is typically assigned based on factors such as being the most common in a population, being an ancestral allele, or being indentified first as a prototypical example of some feature or gene.  For example, 'reference alleles' in characterizing SNPs often represent the allele first characterized in a reference genome, or the most common allele in a population.\n\nIn model organism datasets, 'reference' alleles are typically (but not always) the 'wild-type' variant at a given locus, representing a functional and unaltered version of the feature that is part of a defined genomic background, and against which natural or experimentally-induced alterations are compared."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000512",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000512",
            "label": "allele"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/GENO_0000968",
                "label": "sequence role",
                "type": "sequence_role"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/GENO_0000152",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "GENO_0000152",
                "label": "reference"
            }
        }
    ],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
                    "Entity",
                    "Individual",
                    "pub"
                ],
                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
        }
    ]
}