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Table 2 Comparisons of call rates and concordance on HapMap samples for rare variants under 600, 1500, and 3000 simulated observations and the allocation design 2:1

From: M3-S: a genotype calling method incorporating information from samples with known genotypes

SNPs # SNP Item M3-S M3-S M3-S  
    600 1500 3000  
MAF < 0.1 4364 Call Rate 99.69 99.65 99.59  
   Accuracy 99.33 99.24 99.22  
MAF < 0.05 2329 Call Rate 99.72 99.71 99.68  
   Accuracy 99.34 99.26 99.28  
MAF < 0.01 597 Call Rate 99.59 99.86 99.81  
   Accuracy 99.04 99.06 99.23  
  1. Note: M3-S: M3 incorporating samples with known genotypes; Call Rate: the percentage of valid genotypes; Accuracy: the percentage of consistent genotype; # SNP: the number of SNPs whose MAFs are less than 0.1, 0.05 or 0.01, respectively