genomic genotype (sex-agnostic) A genomic genotype that does not specify the sex determining chromosomal features of its bearer (i.e. does not indicate the background sex chromosome complement) organismal genotype sex-agnostic intrinsic genotype genotype Example zebrafish intrinsic genotype: Genotype = fgf8a<ti282a/+>; shha<tb392/tb392> (AB) reference component (genomic background) = AB variant component ('genomic variation complement') = fgf8a<ti282a/+>; shha<tb392/tb392> . . . and within this variant component, there are two 'variant single locus complements' represented: allele complement 1 = fgf8a<ti282a/+> allele complement 2 = shha<tb392/tb392> and within each of these 'variant single locus complements' there is one or more variant gene locus member: in complement 1: fgf8a<ti282a> in complement 2: shha<ttb392> This modeling approach allows use to create separate genotype instances for data sources that report sex-specific phenotypes to ensure that sex-specific G2P differences are accurately described. These sex-qualified genotypes can be linked to the more general sex-agnostic intrinsic genotype that is shared by make and female mice of the same strain, to aggregate associated phenotypes at this level, and allow aggregation with G2P association data about the same strains from sources that distinguish sex-specific phenotypes (e.g. IMPC) and those that do not (e.g. MGI). Conceptually, a sex-qualified phenotype represents a superset of sequence features relative to a sex-agnostic intirnsic genotype, in that if specifies the background sex-chromosome complement of the genome. Thus, in the genotype partonomy, a sex-qualified genotype has as part a sex-agnostic genotype. This allows for the propagation of phenotypes associated with a sex-qualified genotype to the intrinsic genotype. In practice, most genotype instances classified as sex-agnostic genotypes because they are not sex-specific. When a genotype is indicated to be that of a male or female, it implies a known sex chromosome complement in the genomic background. This requires us to distinguish separate 'sex-qualified' genotype instances for males and females that share a common 'sex-agnostic' genotype. For example, male and female mice that of the same strain/background and containing the same set of genetic variations will have the same sex-agnostic intrinsic genotype, but different sex-qualified intrinsic genotypes (which take into account background sex chromosome sequence as identifying criteria for genotype instances). genomic genotype