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Table 1 Analysis results for the 95% confidence sets of loci contributing to the quantitative phenotype Q2

From: Confidence set of putative quantitative trait loci in whole genome scans with application to the Genetic Analysis Workshop 17 simulated data

    

Causative SNPse

Noncausative SNPsf

Data seta

h b

TDRc

FDRd

Mean

SD

Mean

SD

Single (697)

0.176

0.025 (0.020)

0.050

0.33

0.13

1.40

0.49

 

0.250

0.000 (0.000)

0.000

0.00

0.00

0.00

0.00

Double (1,394)

0.092

0.180 (0.160)

0.050

0.83

0.10

0.30

0.15

 

0.120

0.040 (0.040)

0.000

1.00

0.00

0.00

0.00

Triple (2,091)

0.058

0.697 (0.515)

0.045

1.18

0.08

0.41

0.14

 

0.086

0.076 (0.076)

0.000

1.00

0.00

0.00

0.00

Quadruple (2,788)

0.045

0.860 (0.640)

0.040

1.36

0.09

0.44

0.16

 

0.060

0.540 (0.520)

0.000

1.07

0.05

0.04

0.04

  1. The results are based on 200 single, 100 double, 66 triple, and 50 quadruple replicates.
  2. a Number of original replicates combined to form the new data set to be analyzed. The number in parentheses corresponds to the number of individuals in the sample.
  3. b Threshold for contribution of a putative locus to the total additive genetic variance.
  4. c Proportion of replicates for which the resulting 95% confidence set includes at least one trait locus. Numbers in parentheses give the proportion of replicates for which the resulting confidence sets include only trait loci.
  5. d Proportion of replicates for which the resulting 95% confidence set includes only noncausative SNPs.
  6. e Observed mean and standard deviation (SD) of the number of causative SNPs included in the resulting 95% confidence sets per replicate.
  7. f Observed mean and standard deviation (SD) of the number of non-causative SNPs included in the resulting 95% confidence sets per replicate.