Standard table structure

All steps beyond those in: oscar_colony.colony_management rely on having data in a standard table format.

Example of format for a line with 2 mutations:

ID_offspring	line_name	date_of_birth	ID_father_1	ID_mother_1	sacrifice_reason	n_mutations	mutation_1	mutation_2	genotype_offspring	genotype_father	genotype_mother
ID-001	Line-AB	15/12/2025	ID-F1	ID-M1	End of experiment	2	Mut-A	Mut-B	hom_hom	het_hom	hom_het
ID-002	Line-AB	15/12/2025	ID-F1	ID-M1	End of experiment	2	Mut-A	Mut-B	wt_wt	wt_wt	wt_wt
ID-003	Line-AB	02/01/2026	ID-F1	ID-M1	End of experiment	2	Mut-A	Mut-B	wt_het	wt_hom	wt_wt

Each row represents one animal with columns:

• ID_offspring: the ID of the animal

• line_name: the name of the line

• date_of_birth: date of birth

• ID_father_1: the ID of the animal’s father

• ID_mother_1: the ID of the animal’s mother

• sacrifice_reason: a description of why the animal was sacrificed

• n_mutations: the number of mutations the line has. This should match the number of mutation_NUMBER columns (see below)

• mutation_1 / mutation_2…: the names of the mutations for this line (these should be identical, and in the same order, across all animals from the same line)

  For all genotype columns below, the number of values is equal to n_mutations and is given in the order of the mutation names mutation_1, mutation_2…:

• genotype_offspring: the genotype of the animal. wt, het or hom only, separated by underscores.

• genotype_father: the genotype of the animal’s father. wt, het or hom only, separated by underscores.

• genotype_mother: the genotype of the animal’s mother. wt, het or hom only, separated by underscores.

Mutations

Any number of mutations is supported, just make sure it is consistent throughout all animals belonging to a particular line.

For example, to update the table above for a line with 3 mutations, you would:

• Add another column for mutation_3

• Update n_mutations to 3

• Update all genotype columns to contain 3 values e.g. wt_het_hom, het_hom_hom…

Parents

In the example above, all animals had one father and one mother - but OSCaR does support multi-parent scenarios. For example, you may have put two female animals together with one male for a particular mating. This can be represented by adding further columns for the extra parent ids e.g.:

ID_offspring	line_name	date_of_birth	ID_father_1	ID_mother_1	ID_mother_2	sacrifice_reason	n_mutations	mutation_1	mutation_2	genotype_offspring	genotype_father	genotype_mother
ID-001	Line-AB	15/12/2025	ID-F1	ID-M1	ID-M2	End of experiment	2	Mut-A	Mut-B	hom_hom	het_hom	hom_het

Here we have added one extra column for ID_mother_2.

Note: there should still only be one genotype_mother and one genotype_father column, as the genotypes of all parents of the same sex should be identical. If they are not, then there’s no unambiguous way of determining the breeding scheme that animal came from.

All animals must have at least one mother and one father listed.

Un-genotyped animals

Un-genotyped animals can also be included by leaving the genotype_offspring value empty for a particular row. These animals will still be included in appropriate parts of the LineStatistics.