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. Author manuscript; available in PMC: 2016 May 7.
Published in final edited form as: J Hum Genet. 2015 Sep 17;60(12):729–738. doi: 10.1038/jhg.2015.110

Table 1.

The empirical type I error rates×105, and 106 of TSIR for identifying a CV with MAF of 0.2 associated with the binary and continuous phenotype at α1=0.001 and 0.0001, respectively and using cut-off of r=20 in discovery-replication process

Binary Phenotype
α1 0.001 0.0001
Proportion in Discovery Cohort Proportion in Discovery Cohort
N1 N0/N1 pA Prev. 0.3 0.4 0.5 0.6 0.7 0.3 0.4 0.5 0.6 0.7
250 1.0 0.2 0.30 0.07 1.3 3.1 3.6 3.9 0 0.00 0.6 2.1 2.3
250 2.5 0.2 0.30 0.18 1.9 3.5 4.0 4.3 0 0.40 1.6 2.5 3.6
250 4.0 0.2 0.30 0.33 2.0 3.4 4.2 4.3 0 0.10 1.8 3.2 4.3
250 1.0 0.2 0.10 0.05 1.3 3.0 3.6 3.9 0 0.10 0.6 1.7 3.0
250 2.5 0.2 0.10 0.20 1.6 3.2 3.9 4.2 0 0.00 1.2 2.8 3.4
250 4.0 0.2 0.10 0.26 1.7 3.4 3.9 4.3 0 0.40 1.3 2.2 2.7
250 1.0 0.2 0.01 0.07 1.2 2.8 3.6 3.9 0 0.00 0.8 1.8 2.7
250 2.5 0.2 0.01 0.26 2.0 3.7 4.4 4.7 0 0.30 1.8 4.0 4.4
250 4.0 0.2 0.01 0.39 2.3 4.1 4.6 4.8 0 0.00 1.1 3.2 3.9
550 1.0 0.2 0.30 0.36 1.3 2.6 3.1 3.2 0 0.00 0.2 0.6 1.3
550 2.5 0.2 0.30 0.25 2.1 3.8 4.4 4.6 0 0.30 1.9 3.4 3.9
550 4.0 0.2 0.30 0.25 2.1 3.8 4.4 4.7 0 0.20 2.2 2.9 4.0
550 1.0 0.2 0.10 0.20 1.8 3.5 4.0 4.1 0 0.10 1.3 2.3 3.3
550 2.5 0.2 0.10 0.32 2.2 4.0 4.5 4.9 0 0.30 1.8 2.9 3.4
550 4.0 0.2 0.10 0.41 2.2 3.9 4.3 4.6 0.1 0.40 2.3 4 5.0
550 1.0 0.2 0.01 0.22 1.9 3.3 4.0 4.2 0 0.30 1.7 2.8 4.2
550 2.5 0.2 0.01 0.42 2.5 4.2 4.7 5.0 0 0.40 2.0 3.4 4.1
550 4.0 0.2 0.01 0.54 2.5 4.3 4.8 5.1 0 0.80 2.6 3.9 4.3
1000 1.0 0.2 0.30 0.24 2.0 3.9 4.5 4.6 0 0.20 1.9 3.3 4.0
1000 2.5 0.2 0.30 0.37 2.2 3.9 4.5 4.5 0 0.40 1.9 3.6 3.6
1000 4.0 0.2 0.30 0.40 2.2 3.9 4.7 4.7 0 0.24 1.5 3.8 4.3
1000 1.0 0.2 0.10 0.32 2.0 3.7 4.3 4.5 0.1 0.20 2.0 3.3 4.6
1000 2.5 0.2 0.10 0.32 2.1 3.6 4.2 4.4 0 0.10 1.8 3.0 4.3
1000 4.0 0.2 0.10 0.35 2.4 3.9 4.5 4.8 0 0.60 2.0 4.5 4.4
1000 1.0 0.2 0.01 0.32 2.2 3.8 4.4 4.8 0 0.50 2.2 4.1 4.9
1000 2.5 0.2 0.01 0.46 2.4 3.9 4.6 4.7 0 0.10 2.3 3.9 4.9
1000 4.0 0.2 0.01 0.42 2.6 4.3 4.7 4.9 0 0.40 2.2 3.5 4.1
Continuous Phenotype
α1 0.001 0.0001
Proportion in Discovery Cohort Proportion in Discovery Cohort
N pA 0.3 0.4 0.5 0.6 0.7 0.3 0.4 0.5 0.6 0.7
500 0.2 0.37 2.3 4.3 4.6 4.9 0.1 0.80 2.6 3.4 4.7
700 0.2 0.33 2.5 4.0 4.6 4.8 0 0.50 2.4 3.9 4.9
900 0.2 0.35 2.4 4.2 4.9 5.1 0 0.20 1.5 3.6 4.3
1100 0.2 0.35 2.2 4.0 4.5 4.7 0 0.20 2.1 3.3 4.6
2000 0.2 0.39 2.2 4.0 4.4 4.7 0 0.60 2.6 4.3 4.3
500 0.05 0.45 2.4 4.0 4.8 4.9 0.12 0.47 3.1 5.2 6.0
700 0.05 0.45 2.3 3.9 4.6 4.9 0 0.80 2.5 3.7 4.0
900 0.05 0.52 2.7 4.6 5.3 5.4 0 0.70 2.7 5.1 5.6
1100 0.05 0.37 2.3 3.9 4.5 4.7 0 0.50 1.7 3.0 3.6
2000 0.05 0.46 2.4 4.4 5.1 5.2 0 0.50 1.9 3.4 3.9