The Korean donor's haplotypes was predicted with the HapMap CHB/JPT population
Don't use the following paragraph. It was from the BGI article.
We used PHASE and the available phased genotypes of the HapMap CHB/JPT population to predict the YH genome haplotypes. The700,320 YH genome heterozygotes that overlapped with HapMap loci were used to construct 4,399 haplotype blocks that averaged 587?kb in size (Fig. 4). Of these heterozygous SNPs, 3,039 (0.43%) showed an inconsistent phase in the two adjacent fragments, which may potentially break the haplotype blocks. Additional potential haplotype breakpoints were 1,021,953 heterozygous YH genome SNPs absent in the HapMap. We evaluated this by checking paired-end reads that simultaneously covered two of the heterozygotes used in phasing. A total of 43,902 heterozygous SNP pairs were covered by read pairs, among which 97.37% (42,746 pairs) were in agreement with haplotypes as the corresponding covered read pairs. In total, the 2,434 haplotypes that had sizes greater than 200 kb covered 2.38?Gb of the genome.
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