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Table 1 Results summary for 287 HapMap samples and 41 SNPs

From: Robust SNP genotyping by multiplex PCR and arrayed primer extension

Method Call rate Concordance with HapMap
MACGT (0.001 cut-off) + manual calls 98.90% (9% manual calls) 99.94%
LDA (0.75 threshold) Total cases 94.91% (10,523 cases vs. 11,087) 99.91% (10,514 vs. 10,523)
LDA (0.75 threshold) Homozygous cases 95.41% (6,883 vs. 7,214) 99.96% (6,880 vs. 6,883)
LDA (0.75 threshold) Heterozygous cases 93.98% (3,640 vs. 3,873) 99.84% (3,634 vs. 3,640)