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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

From: A simple procedure for directly obtaining haplotype sequences of diploid genomes

  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
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