. 2012 Jul 18;7(7):e40925. doi: 10.1371/journal.pone.0040925

Table 5. LD–Gene Region 2^*.

	Method	N^**	Min	Q1	Median	Q3	Max	Mean	SD
D’	Hapgen	7002401	−1.000	−0.053	<0.001	0.061	1.000	0.002	0.172
	Resampling	7138597	−0.999	−0.018	<0.001	0.032	1.000	0.009	0.073
	HapSim	7149516	−1.000	−0.102	<0.001	0.070	1.000	−0.050	0.224
r²	Hapgen	7002401	−0.861	−0.002	<0.001	0.002	0.666	<0.001	0.013
	Resampling	7138597	−0.250	−0.001	<0.001	0.001	0.359	<0.001	0.005
	HapSim	7149516	−0.934	−0.002	<0.001	0.003	0.333	−0.005	0.040

Change in simulated LD from original HapMap sample LD for each pair of SNPs in Gene Region 2 (LD_simulated – LD_HapMap).

^**

Sum of SNP pairs over all 100 replicates. The number of SNP pairs is not divisible by 100 because monoallelic SNPs were dropped from the LD calculations. Because Hapgen had more variation in MAF, it was more likely that a SNP with a low MAF would become monoallelic in one or more simulation replicates and thus, more SNP pairs were dropped from the LD calculations than for Resampling or HapSim.

Table 5. LD–Gene Region 2*.

Table 5. LD–Gene Region 2^*.