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Variation a owl:Class extends VariationFeature

Subclasses

Annotations

skos:definition Defines a genomic variant
empusa:propertyDefinitions # The type of Variation
type type::VariationTypes;


#
Allele of the alternate sequence
alternate xsd:String;
#
Quality score of the marker
quality xsd:String?;
# Allele of the reference sequence
reference xsd:String?;
#
Variant identification code
ID xsd:String?;
# Variant filter
filter xsd:String?;
#
Average read depth
readDepth xsd:String?;
# Number of Homozygous variant samples
homozygousSamples xsd:Integer?;
#
Number of Heterozygous variant samples
heterozygousSamples xsd:Integer?;
# Number of wildtype samples
wildtypeSamples xsd:Integer?;
#
Number of samples not called
numberNotCalled xsd:Integer?;

# Ancestral Allele
ancestralAllele xsd:String?;
#
Alelle Count
alleleCount xsd:Integer?;
# Frequency in which the alternate allele is found
alleleFreq xsd:String?;
#
total number of alleles in called genotypes
alleleNumber xsd:Integer?;
# RMS base quality
baseQuality xsd:String?;
#
Cigar string describing alignment of alternate allele to reference
CIGAR xsd:String?;
# dbSNP membership
dbSNP xsd:String?;
#
End position of the variant described in this record (for use with symbolic alleles)
end xsd:Long?;
# Mapping Quality
mapQuality xsd:String?;
#
Number of samples with data
numberOfSamples xsd:Integer?;
# Strand bias
strandBias xsd:String?;
#
Validated
validated xsd:String?;


# Genotypes of the sample the variant was called on
genotype @:VariantGenotype
;
rdfs:label Variation

Properties

property description cardinality type
reference Allele of the reference sequence 0:1 xsd:String
genotype Genotypes of the sample the variant was called on 0:N VariantGenotype
type The type of Variation 1:1 VariationTypes
homozygousSamples Number of Homozygous variant samples 0:1 xsd:Integer
validated Validated 0:1 xsd:String
end End position of the variant described in this record (for use with symbolic alleles) 0:1 xsd:Long
readDepth Average read depth 0:1 xsd:String
numberOfSamples Number of samples with data 0:1 xsd:Integer
mapQuality Mapping Quality 0:1 xsd:String
alleleFreq Frequency in which the alternate allele is found 0:1 xsd:String
ancestralAllele Ancestral Allele 0:1 xsd:String
quality Quality score of the marker 0:1 xsd:String
numberNotCalled Number of samples not called 0:1 xsd:Integer
alleleNumber total number of alleles in called genotypes 0:1 xsd:Integer
alleleCount Alelle Count 0:1 xsd:Integer
strandBias Strand bias 0:1 xsd:String
heterozygousSamples Number of Heterozygous variant samples 0:1 xsd:Integer
alternate Allele of the alternate sequence 0:N xsd:String
dbSNP dbSNP membership 0:1 xsd:String
CIGAR Cigar string describing alignment of alternate allele to reference 0:1 xsd:String
ID Variant identification code 0:1 xsd:String
filter Variant filter 0:1 xsd:String
wildtypeSamples Number of wildtype samples 0:1 xsd:Integer
baseQuality RMS base quality 0:1 xsd:String