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

Ferdosi, Mohammad H; Kinghorn, Brian P; van der Werf, Julius H J; Gondro, Cedric

doi:10.1186/1297-9686-46-11

Genetics Selection Evolution

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

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.

Back to article page

ISSN: 1297-9686

Contact us

Submission enquiries: helene.hayes@inrae.fr
General enquiries: info@biomedcentral.com