A simple procedure for directly obtaining haplotype sequences of diploid genomes

BMC Genomics

Table 3 Haplotype consistency after using five different maximum gap lengths for joining contigs into scaffolds. Haplotype consistency with and without corrections for switch errors for five different maximum gap lengths for joining contigs into scaffolds for chromosome one. The consistency values for all chromosomes with the default distance of 1000 is shown in the top line for comparison. The relative low value of consistency for the whole genome against SNP haplotypes (0.88) is due to three chromosomes with low consistencies (0.60–0.66), all other consistencies were > 0.87 and the median was 0.917. The consistencies obtained after using TargetCut to generate scaffolds is also shown. The N50 haplotype length obtained using SIH shows the large effect of increasing threshold gap length between contigs

	Against Other Scaffolds		Scaffolds Against HD SNP haplotypes		SIH phase haplotypes against HD SNP haplotypes		N50 SNP Haplotype Length (Mb)
Gap	Consistency	Switch Consistency	Consistency	Switch Consistency	Consistency	Switch Consistency	N50 SNP Haplotype Length (Mb)
All 1000	0.991	0.997	0.959	0.980	0.886	0.969	97
Chr1 1000	0.990	0.996	0.960	0.978	0.927	0.973	99
Chr1 2000	0.987	0.995	0.939	0.972	0.881	0.969	242
Chr1 3000	0.986	0.995	0.918	0.969	0.836	0.967	394
Chr1 4000	0.985	0.995	0.898	0.963	0.823	0.962	564
Chr1 5000	0.983	0.994	0.891	0.960	0.822	0.964	592
Chr1 TargetCut	0.988	0.995	0.942	0.971	0.894	0.969	223

ISSN: 1471-2164