Table 1  Transition probabilities between any given set of markers
Founder state at position 1Founder state at position 2Transition probability
iiiier + 0.95 ⋅ (1 − er) ⋅ 1/8
jj1/8 ⋅ 0.95 ⋅ (1 − er)
ij1/7 ⋅ 0.05 ⋅ (1 − er)
jk0
ijijer + 2 ⋅ 0.05 ⋅ (1 − er) ⋅ 1/14
ii or jj(1 − er) ⋅ 1/2 ⋅ 0.85
ik or jk(1 − er) ⋅ 1/14 ⋅ 0.15
kl0
• General founder genotypes are represented by i, j, k, and l with different letters denoting different founders: e.g., ii represents a homozygous founder genotype while ij denotes a heterozygous founder genotype, with i and j representing different founders. r is the probability of a recombination event occurring in the interval and is equal to X chromosome: 33*d*(1/10) Autosomes: 25*d*(1/10), where d is the genetic distance between any pair of markers (interpolated from FlyBase).