Table 3

Variance components estimated from datasets generated by permutation, simulation with linkage equilibrium in founders (LE simulation), and simulation with initial linkage disequilibrium (LD simulation), and thresholds for 10-SNP window variances based on 10% and 20% chromosome-wise type I error rates.

Methods

Variance Components

Window variance threshold


Genotypic

Residual

Total

10%

20%

Permutation

3.15

98.59

101.74

0.0011

0.0009

LE simulation

20.83

79.84

100.67

0.0204

0.0094

LD simulation

17.14

83.40

100.55

0.1645

0.0887

Original1

47.13

53.48

100.61


1Estimated from the original QTLMAS2010 dataset using BayesCπ, training on the first 4 generations.

Sun et al. BMC Proceedings 2011 5(Suppl 3):S13   doi:10.1186/1753-6561-5-S3-S13

Open Data