VariantGenotype a owl:Class extends VariationFeature
Subclasses
Annotations
| skos:definition | Defines a genotype for a called Variation in the Variation class |
| empusa:propertyDefinitions | # Genotype of a sample for a specific variant genotype xsd:String?; # Genotype quality genotypeQuality xsd:String?; # Raw read depth readDepth xsd:String?; # Read depth quality depthQuality xsd:String?; # Read depth of reference base refDepth xsd:String?; # Read depth of alternate base altDepth xsd:String?; # p-value from Fisher's Exact Test pVal xsd:String?; # Allele frequency freq xsd:String?; # genotype filter filter xsd:String?; # Genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields likelihood xsd:String?; #phred scaled likelihood phredLikelihood xsd:Integer?; #phred probabilities phredProb xsd:Float?; #Haplotype qualities haploQuality xsd:String?; #Phase set phaseSet xsd:String?; # Phase quality phaseQuality xsd:Integer?; #Expected allele counts(comma seperated) expectedAlleleCounts xsd:String?; #Mapping Quality mapQuality xsd:Integer?; # Reference Organism refOrganism @:Organism?; #* Alternative Organism altOrganism @:Organism?; |
Properties
| property | description | cardinality | type |
|---|---|---|---|
| expectedAlleleCounts | Expected allele counts(comma seperated) | 0:1 | xsd:String |
| genotype | Genotype of a sample for a specific variant | 0:1 | xsd:String |
| altOrganism | Alternative Organism | 0:1 | Organism |
| altDepth | Read depth of alternate base | 0:1 | xsd:String |
| phredLikelihood | phred scaled likelihood | 0:1 | xsd:Integer |
| readDepth | Raw read depth | 0:1 | xsd:String |
| mapQuality | Mapping Quality | 0:1 | xsd:Integer |
| depthQuality | Read depth quality | 0:1 | xsd:String |
| likelihood | Genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields | 0:1 | xsd:String |
| genotypeQuality | Genotype quality | 0:1 | xsd:String |
| refDepth | Read depth of reference base | 0:1 | xsd:String |
| haploQuality | Haplotype qualities | 0:1 | xsd:String |
| phaseSet | Phase set | 0:1 | xsd:String |
| pVal | p-value from Fisher's Exact Test | 0:1 | xsd:String |
| phaseQuality | Phase quality | 0:1 | xsd:Integer |
| filter | genotype filter | 0:1 | xsd:String |
| phredProb | phred probabilities | 0:1 | xsd:Float |
| freq | Allele frequency | 0:1 | xsd:String |
| refOrganism | Reference Organism | 0:1 | Organism |