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Linkage Disequilibrium-Based Quality Control for Large-Scale Genetic Studies

Figure 3

LD-based error rate vs. HWE.

An LD-based error rate was estimated and a test of HWE (PEDSTATS [13]) was conducted for data from chromosome 7 HapMap CEU unrelated samples at each of the following types of SNPs: passed all HapMap QC criteria and had zero MIs (black ○); passed QC criteria with exactly one MI (green +); and failed due to the presence of multiple MIs (red ♦). SNPs which failed QC due to extreme deviations from HWE are excluded.

Figure 3