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# Breeding

## Parameters of the Breeding Calculator

Number of required animals (genotypes_N): The number of animals at weaning age that is to be obtained with the set confidence.

Confidence: Likelihood of successfully obtaining the required number of animals.

Mendelian success probability (desired_genotype_p): Percentage of offspring of the desired genotype determined by e.g., the Punnett square. Also, deviations (e.g., partial fetal death) from the classical Mendelian percentages can be used. Examples of online Punnett square calculators are Punnett 1 and Punnett 2.

Fertility: Percentage of breeding couples of a particular strain/line which gives birth to at least one litter brings the pups to weaning age; if animals at different ages need to be used (e.g., fetuses, newborns, or aged) this number needs to be adjusted accordingly. If a pair was proven fertile, this parameter can be set to 100%.

Litter size (litter_average): The mean litter size at weaning age of a particular strain or line; if animals at different age need to be used (e.g., fetuses, newborns, or aged) this number needs to be adjusted accordingly.

Sex (sex_distribution): The researcher can either choose to use all of one sex or both sexes. In the latter case either equal numbers of males and females (a balanced design) or all animals can be used. If the sex ratio of a particular cross is deviating from the 50% norm, in the sex settings all animals should be used. Sex can then be treated as a gene with two alleles in a heterozygous (males) with homozygous (females) cross and respective parameters set (e.g., 0.4 and 0.6 for the two possible outcomes).

Birth span (birth_days): This parameter gives the age span that the animals are allowed to have when taken from the breedings for use in experiment or otherwise. Unless the researcher wants to perform a study with a particularly narrow age range (1,2, or 3 days) the value should be set to 4 or more (the ouput makes sense to approximately three weeks at which time the next generation of pups may be born).

### Actual breeding parameters used in the calculator

STRAIN FERTILITY MEAN LITTER SIZE
129/SvJa 0.75 5.9
A/J 0.65 6.3
AKR/J 0.84 6.1
BALB/c 0.47 5.2
C3H/HeJ 0.86 5.7
C3H/HeOuJ 0.99 6.4
C57BL/6J 0.84 7.0
C57BL/610SnJ 0.67 6.3
CBA/CaJ 0.96 6.9
DBA/2J 0.75 5.4
FVB/N 0.90 9.5
SJL/J 0.72 6.0

According to: http://www.informatics.jax.org/silver/tables/table4-1.shtml