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Table 2 R 2 +/- standard deviation across replicates between inferred and true haplotypes

From: Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes

  Half-sib family size
  4 6 8 10 20 40
1250 SNPs
R 2 0.955 ± 0.034 0.923 ± 0.056 0.918 ± 0.048 0.913 ± 0.040 0.917 ± 0.036 0.934 ± 0.021
SWR 0.043 ± 0.035 0.055 ± 0.040 0.059 ± 0.037 0.057 ± 0.031 0.046 ± 0.020 0.034 ± 0.010
HI% 0.704 ± 0.056 0.815 ± 0.047 0.877 ± 0.044 0.903 ± 0.031 0.975 ± 0.008 0.985 ± 0.005
R 2 e 0.932 ± 0.035 0.896 ± 0.055 0.894 ± 0.052 0.888 ± 0.043 0.894 ± 0.033 0.907 ± 0.022
SWRe 0.075 ± 0.044 0.080 ± 0.037 0.079 ± 0.037 0.078 ± 0.030 0.064 ± 0.017 0.050 ± 0.010
HIe% 0.708 ± 0.054 0.821 ± 0.046 0.877 ± 0.041 0.907 ± 0.027 0.976 ± 0.007 0.987 ± 0.005
5000 SNPs
R 2 0.977 ± 0.026 0.969 ± 0.031 0.960 ± 0.029 0.961 ± 0.025 0.969 ± 0.014 0.975 ± 0.010
SWR 0.015 ± 0.018 0.018 ± 0.017 0.022 ± 0.009 0.023 ± 0.015 0.015 ± 0.009 0.008 ± 0.003
HI% 0.644 ± 0.159 0.800 ± 0.047 0.863 ± 0.037 0.900 ± 0.030 0.980 ± 0.009 0.990 ± 0.007
R 2 e 0.933 ± 0.057 0.934 ± 0.036 0.923 ± 0.029 0.925 ± 0.038 0.943 ± 0.015 0.947 ± 0.014
SWRe 0.044 ± 0.023 0.042 ± 0.015 0.045 ± 0.010 0.047 ± 0.018 0.032 ± 0.009 0.022 ± 0.003
HIe% 0.680 ± 0.044 0.806 ± 0.040 0.864 ± 0.032 0.905 ± 0.025 0.981 ± 0.010 0.991 ± 0.008
10 000 SNPs
R 2 0.977 ± 0.022 0.971 ± 0.025 0.958 ± 0.035 0.979 ± 0.013 0.977 ± 0.009 0.980 ± 0.009
SWR 0.012 ± 0.015 0.015 ± 0.007 0.018 ± 0.015 0.010 ± 0.006 0.007 ± 0.003 0.004 ± 0.001
HI% 0.680 ± 0.028 0.781 ± 0.035 0.867 ± 0.025 0.915 ± 0.032 0.983 ± 0.008 0.993 ± 0.004
R 2 e 0.954 ± 0.024 0.937 ± 0.027 0.926 ± 0.037 0.944 ± 0.030 0.948 ± 0.012 0.954 ± 0.011
SWRe 0.035 ± 0.015 0.038 ± 0.008 0.039 ± 0.017 0.029 ± 0.006 0.022 ± 0.004 0.017 ± 0.001
HIe% 0.682 ± 0.029 0.783 ± 0.036 0.871 ± 0.025 0.919 ± 0.029 0.986 ± 0.005 0.996 ± 0.001
  1. Switch error rate (SWR) and percentage of assigned results (HI%) using simulated data (dataset B) on 120 half-sib families with varying numbers of offspring per family (between 4 and 40) and different SNP marker densities (1250, 5000 and 10 000); e suffix is for a 1% genotyping error.