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Table 2 Top Regression Power Results

From: Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

Program Power Length Est kb Het α β d' LD-pruning
Autozygosity within 20 generations (low genotyping error)
PLINK 0.696 50 SNPs 1108 0 0.003 0.33 3.19 Moderate
PLINK 0.691 80 SNPs 919 0 0.003 0.31 3.2 Light
PLINK 0.670 55 SNPs 1219 0 0.002 0.45 3.02 Moderate
PLINK 0.662 80 SNPs 918 1 0.005 0.23 3.28 Light
Autozygosity within 20 generations (high genotyping error)
PLINK 0.657 45 SNPs 949 0 0.004 0.29 3.19 Moderate
PLINK 0.636 55 SNPs 1160 0 0.002 0.47 2.97 Moderate
PLINK 0.628 50 SNPs 1054 0 0.003 0.37 3.07 Moderate
PLINK 0.608 60 SNPs 1265 1 0.003 0.41 3.01 Moderate
Autozygosity within 50 generations (low genotyping error)
PLINK 0.725 65 SNPs 746 0 0.005 0.40 2.83 Light
PLINK 0.712 50 SNPs 574 0 0.01 0.23 3.06 Light
PLINK 0.710 60 SNPs 689 0 0.006 0.36 2.88 Light
PLINK 0.709 45 SNPs 517 0 0.012 0.18 3.14 Light
Autozygosity within 50 generations (high genotyping error)
PLINK 0.671 35 SNPs 738 0 0.007 0.38 2.76 Moderate
PLINK 0.652 40 SNPs 844 0 0.004 0.47 2.69 Moderate
PLINK 0.649 45 SNPs 949 0 0.003 0.55 2.64 Moderate
PLINK 0.649 80 SNPs 777 1 0.006 0.40 2.73 Light
  1. Listed are the top four repression power results for detecting autozygosity within the past 20 and 50 generations, and within low and high SNP genotyping error. Low genotyping error = 0.2% genotyping error rate. High genotyping error = 1% genotyping error rate. Length = Minimum SNP or cM length to call a segment. Est kb = Minimum expected kb distance for the given length. Het = Number of Heterozygotes allowed in a segment. α= Type 1 error rate. β= Type 2 error rate. d'= d-prime estimate. LD-pruning = Level of LD-pruning. Moderate = Removal of SNPs within a 50 SNP window that had VIF greater than 2 (i.e. --indep 50 5 2 in PLINK). Light = Removal of SNPs within a 50 SNP window that had VIF greater than 10 (i.e. --indep 50 5 10 in PLINK).
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