Applying LRP in a simple and conservative manner, i.e. only individuals who share IBS ≥ 1 for the entire extended region with a proband are considered as potential surrogate parents, 1995 (5.6%) of the 35,528 typed individuals were not phased at all either because no surrogate parents were identified for them initially or putative surrogate parents identified were eliminated later in the phasing process due to incompatibilities (Methods). Among the others, 30,954 (87.1% of the total) were phased for every SNP, and 2579 (7.3%) were phased for 90.4% of the heterozygous genotypes (Table 2). Overall, counting all 35,528 individuals, the proportion of heterozygous SNPs phased (yield) was 93.7% (16,201,012 out of 17,287,391). There are 2839 father-mother-offspring trios among the typed individuals. To empirically evaluate the accuracy of our phasing method, we removed the parents (3826 individuals) in these trios from the list of typed individuals. Because some of the removed parents are themselves offspring in typed trios, 2718 offspring were left. We phased these 2718 offspring/probands by (1) applying LRP to the reduced list of 31,702 individuals, and compared the
