Skip to content

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