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Inconsistent pair (IP) depth counts those read pairs that map inconsistently; that is, they do not meet the CP criteria.
If you write down the rule for what makes two triples inconsistent with one another, and then you write a program to generate all configurations that have no inconsistent pair, then you get only 2²¹ configurations that have no inconsistencies.
The most likely reason is that, in our implementation, the PAR-OFF test deleted only one animal of an inconsistent pair when at least one of the animals was linked to more than one inconsistent parent-offspring pair.
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For each haplotype block, we count the consistent and inconsistent pairs.
For each haplotype segment, we count the consistent and inconsistent pairs.
The total numbers of consistent and inconsistent pairs over all the haplotype segments are denoted by CP and IP, respectively.
The total numbers of consistent and inconsistent pairs over all the haplotype blocks are denoted by CP and IP, respectively.
If these assumptions are satisfied, the Bayesian score can be further developed for consistent pairs 〈ℳ,ℐ〉: For inconsistent pairs the score is −∞.
Empirical distributions of the number of opposing homozygous loci were used to define minimum thresholds for declaring inconsistent pairs of unrelated animals, half-sibs, and full-sibs.
Detection of inconsistent pairs of sibs was either based on differences between pedigree and genomic relationships (SIBREL), or on the number of opposing homozygous genotypes (SIBCOUNT) between them.
In the first step, all inconsistent pairs were identified and in subsequent steps, the animal with the highest number of inconsistencies was iteratively removed from the dataset until no inconsistencies remained.
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