Conditional probabilities of descent, Pr(Embedded Image) and Pr(Embedded Image), of the maternal allele (Embedded Image) of individual i from the maternal (Embedded Image) and paternal (Embedded Image) allele of its mother d at HD-SNP k, depending on segregation indicators at the left (Embedded Image) and the right (Embedded Image) LD-SNP of an adjacent pair on the maternal haplotype of individual i

Embedded ImageEmbedded ImagePrEmbedded ImagePrEmbedded Image
00(1 – θlk)(1 – θkr)/(1 – θlr)θlkθkr/(1 – θlr)
01(1 – θlkkrlrθlk(1 – θkr)/θlr
10θlk(1 – θkr)/θlr(1 – θlkkrlr
11θlkθkr/(1 – θlr)(1 – θlk)(1 – θkr)/(1 – θlr)
  • θlkkr), recombination frequency between HD-SNP k and the left (right) LD-SNP; θlr, recombination frequency between left and right LD-SNPs; Embedded Image (1) means grandmaternal (grandpaternal) origin.