Investigation of altering single-nucleotide polymorphism density on the power to detect trait loci and frequency of false positive in nonparametric linkage analyses of qualitative traits

Table 4 Type I error count in simulated data for full dataset

Trait	Marker set	Pop. dz. freq.	# of replicates with data^a	Mean number of false positives below p-value criterion of^b
				0.05	0.01	0.0017	0.001	0.0001	0.000049
Dominant
D8044	MS 7.5 cM	0.06	300	8.10	1.92	0.18	0.08	0	0
	SNP 3 cM			7.73	1.79	0.16	0.09	0	0
D8050	MS 7.5 cM	0.18	300	7.63	1.82	0.53	0.38	0.03	0.02
	SNP 3 cM			7.33	2.11	0.47	0.30	0.03	0.02
D8051	MS 7.5 cM	0.50	300	7.48	2.56	0.45	0.30	0.04	0.02
	SNP 3 cM			7.22	2.19	0.45	0.30	0.04	0.02
Recessive
R8045	MS 7.5 cM	0.08	300	8.59	2.36	0.29	0.16	0.01	0
	SNP 3 cM			8.11	2.23	0.25	0.14	0.01	0
R8050	MS 7.5 cM	0.01	229	2.66	0.06	0	0	0	0
	SNP 3 cM			2.20	0.03	0	0	0	0
R8051	MS 7.5 cM	0.22	300	7.57	2.02	0.39	0.27	0.03	0.02
	SNP 3 cM			7.44	2.03	0.47	0.34	0.04	0.01

^aFor rare disease not all replicates contained informative pedigrees.
^bMean number of false positive regions in the 9 unlinked chromosomes per replicate with p- value below the following criteria.

ISSN: 2730-6844