LD–Gene Region 2*.

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

*基因区域2中每对单核苷酸多态性（Single Nucleotide Polymorphism，SNP）的模拟连锁不平衡（Linkage Disequilibrium，LD）与原始HapMap样本连锁不平衡的差值（LDsimulated – LDHapMap）。该差值为所有100次重复实验中各SNP对差值的总和。由于在连锁不平衡计算中剔除了单等位基因SNP，因此SNP对的总数无法被100整除。由于Hapgen工具的次要等位基因频率（Minor Allele Frequency，MAF）变异程度更高，低次要等位基因频率的SNP在一次或多次模拟重复实验中更易变为单等位基因，因此相较于重采样（Resampling）或HapSim方法，本次连锁不平衡计算中剔除的SNP对数量更多。