An illustration of pair consistency. Consistency of pair sites. A. a. We assume that the two true haplotypes are the sequences of all 0 and all 1. b. Inferred haplotypes contain switch errors indicated by the arrows: (i) a consistent pair, (ii) an inconsistent pair, and (iii) if there are an uncontrolled number of switch errors between a pair, the probabilities of being consistent or inconsistent are both 0.5. B. The example of the case that switch error rate is not suitable to evaluate the quality of the segment. The consistency of a reconstructed haplotype which has single switch error in the middle (top) is high than a reconstructed haplotype which has single switch error located at an end of the segment, but switch error rate cannot distinguish these situations. Two contiguous switch errors, which are caused by sequencing error or genotyping error and do not disrupt the consistency between front and back parts, are regarded as twice of a single switch error in switch error rate (bottom).
Matsumoto and Kiryu BMC Genomics 2013 14(Suppl 2):S5 doi:10.1186/1471-2164-14-S2-S5