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Table 1 Error rates obtained according to the level of missing information in the GH1 dataset

From: Computation of haplotypes on SNPs subsets: advantage of the "global method"

GH1
MD Method IER SimER IF Res rate
0% Global_3snp 1.12% 0.37% 0.994 100%
  Local_3snp 1.56% 0.52% 0.9904 100%
  Global_5snp 3.16% 0.65% 0.9834 100%
  Local_5snp 3.57% 0.72% 0.9784 100%
  Global_7snp 4.87% 0.74% 0.9714 100%
  Local_7snp 5.57% 0.83% 0.9704 100%
2% Global_3snp 1.63% 0.38% 0.9937 100%
  Local_3snp 2.57% 0.68% 0.9898 100%
  Global_5snp 4.34% 0.88% 0.9826 100%
  Local_5snp 5.26% 1.20% 0.9792 100%
  Global_7snp 6.83% 0.82% 0.9693 100%
  Local_7snp 8.70% 1.03% 0.961 100%
5% Global_3snp 2.03% 0.46% 0.9934 100%
  Local_3snp 3.65% 0.79% 0.9894 100%
  Global_5snp 5.40% 0.88% 0.98 100%
  Local_5snp 7.68% 1.20% 0.972 100%
  Global_7snp 8.43% 1.07% 0.967 100%
  Local_7snp 11.00% 1.37% 0.959 100%
10% Global_3snp 3.57% 0.73% 0.989 100%
  Local_3snp 6.60% 1.33% 0.983 99.87%
  Global_5snp 8.06% 1.19% 0.973 100%
  Local_5snp 12.91% 1.86% 0.962 100%
  Global_7snp 11.84% 1.35% 0.959 100%
  Local_7snp 16.41% 1.88% 0.946 100%
15% Global_3snp 5.21% 1.01% 0.987 100%
  Local_3snp 9.49% 1.84% 0.977 99.45%
  Global_5snp 10.67% 1.47% 0.97 100%
  Local_5snp 17.00% 2.33% 0.953 100%
  Global_7snp 15.70% 1.67% 0.953 100%
  Local_7snp 21.87% 2.35% 0.931 100%
20% Global_3snp 6.65% 1.26% 0.984 98.44%
  Local_3snp 12.45% 2.41% 0.97 97.02%
  Global_5snp 12.83% 1.72% 0.964 100%
  Local_5snp 22.15% 3.02% 0.936 99.60%
  Global_7snp 18.47% 1.92% 0.946 99.72%
  Local_7snp 26.44% 2.81% 0.916 100%
  1. Summary of the mean error rates obtained by each subhaplotyping method when they used the Rmax resolution produced by PHASE. The average individual error rate (IER) and similarity error rate (SimER) were computed according to the level of missing data (MD) introduced in the population (0%, 2%, 5%, 10%, 15%, 20%). Tests were performed on randomly selected SNP subsets of size 3, 5, and 7 taken out of the 14 SNPs present in the GH1 genomic dataset (see text and Material and Methods). This table presents the average of the IF coefficients which compares the accuracy of the subhaplotypes frequencies found by each subhaplotyping method. The global method fares always better.