Evaluation of linkage disequilibrium and its effect on non-parametric multipoint linkage analysis using two high density single-nucleotide polymorphism mapping panels

Murray, Sarah Shaw

doi:10.1186/1471-2156-6-S1-S85

Table 2 Information content comparisons in the two SNP marker sets and the COGA STR marker set (Average (min, max))

From: Evaluation of linkage disequilibrium and its effect on non-parametric multipoint linkage analysis using two high density single-nucleotide polymorphism mapping panels

Chromosome	Illumina		Affymetrix		COGA STR (all loci)
	all loci	r² < 0.4	all loci	r² < 0.4
1	0.91 (0.75,0.95)	0.91 (0.75,0.96)	0.91 (0.69,0.95)	0.91 (0.69,0.95)	0.64 (0.28,0.90)
2	0.91 (0.79,0.95)	0.91 (0.79,0.95)	0.92 (0.78,0.96)	0.92 (0.77,0.96)	0.70 (0.47,0.90)
3	0.91 (0.82,0.95)	0.91 (0.83,0.95)	0.92 (0.84,0.97)	0.92 (0.83,0.97)	0.59 (0.41,0.86)
4	0.89 (0.72,0.96)	0.89 (0.72,0.95)	0.91 (0.59,0.96)	0.91 (0.59,0.96)	0.62 (0.47,0.78)
5	0.90 (0.77,0.95)	0.90 (0.77,0.95)	0.92 (0.75,0.96)	0.92 (0.75,0.96)	0.63 (0.37,0.85)
6	0.90 (0.72,0.96)	0.90 (0.71,0.95)	0.92 (0.71,0.96)	0.92 (0.71,0.96)	0.60 (0.37,0.84)
7	0.91 (0.78,0.95)	0.91 (0.78,0.95)	0.91 (0.78,0.96)	0.91 (0.77,0.95)	0.78 (0.59,0.92)
8	0.90 (0.79,0.95)	0.89 (0.75,0.95)	0.91 (0.75,0.95)	0.91 (0.75,0.95)	0.67 (0.44,0.87)
9	0.89 (0.78,0.95)	0.89 (0.77,0.95)	0.91 (0.70,0.96)	0.91 (0.69,0.96)	0.62 (0.47,0.85)
10	0.89 (0.78,0.95)	0.89 (0.78,0.95)	0.91 (0.68,0.95)	0.91 (0.68,0.95)	0.48 (0.31,0.76)
11	0.89 (0.66,0.95)	0.89 (0.66,0.95)	0.92 (0.70,0.96)	0.92 (0.69,0.96)	0.51 (0.30,0.74)
12	0.90 (0.75,0.95)	0.89 (0.75,0.95)	0.90 (0.74,0.96)	0.90 (0.74,0.96)	0.65 (0.38,0.90)
13	0.90 (0.77,0.95)	0.89 (0.76,0.95)	0.91 (0.62,0.96)	0.91 (0.62,0.96)	0.62 (0.33,0.86)
14	0.90 (0.79,0.95)	0.89 (0.79,0.95)	0.86 (0.43,0.95)	0.86 (0.42,0.95)	0.62 (0.49,0.79)
15	0.89 (0.77,0.95)	0.89 (0.76,0.95)	0.90 (0.83,0.95)	0.90 (0.83,0.95)	0.67 (0.56,0.85)
16	0.90 (0.75,0.95)	0.89 (0.74,0.95)	0.87 (0.46,0.95)	0.86 (0.46,0.95)	0.57 (0.33,0.82)
17	0.89 (0.79,0.94)	0.88 (0.78,0.94)	0.85 (0.51,0.94)	0.85 (0.51,0.94)	0.56 (0.35,0.77)
18	0.88 (0.75,0.95)	0.88 (0.75,0.95)	0.91 (0.70,0.95)	0.91 (0.70,0.95)	0.51 (0.35,0.69)
19	0.88 (0.73,0.95)	0.86 (0.71,0.94)	0.81 (0.57,0.94)	0.81 (0.56,0.94)	0.56 (0.41,0.76)
20	0.89 (0.82,0.94)	0.89 (0.80,0.94)	0.89 (0.78,0.95)	0.89 (0.71,0.95)	0.60 (0.39,0.82)
21	0.91 (0.85,0.94)	0.90 (0.84,0.94)	0.92 (0.75,0.95)	0.91 (0.75,0.95)	0.59 (0.39,0.83)
22	0.89 (0.79,0.95)	0.88 (0.78,0.95)	0.84 (0.77,0.94)	0.84 (0.77,0.94)	0.55 (0.34,0.76)
X	0.74 (0.33,0.97)	0.72 (0.20,0.97)	0.91 (0.84,0.97)	0.88 (0.78,0.95)	0.32 (0.24,0.40)
Genome	0.89 (0.33,0.97)	0.89 (0.20,0.96)	0.90 (0.43,0.97)	0.90 (0.42,0.97)	0.61 (0.24,0.92)
No. chr w/avg IC < 0.8	1	1	0	0	23
No. chr w/min IC < 0.7	2	2	8	10	23

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