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Table 7 Scenario with phenocopies.

From: Linkage disequilibrium interval mapping of quantitative trait loci

Marker type

MSE

Difference in MSE P value

 

T2

HAPim

 

Phenocopy rate = 15% b

SNP(1)

2.65

2.03

0.021*

MST(2)

0.84

0.35

< 0.001**

Phenocopy rate = 30%

SNP(1)

4.90

3.29

< 0.001**

MST(2)

1.94

0.67

< 0.001**

  1. * : P < 0.05, ** : P < 0.01
  2. b: Phenocopy rate refers to the percentage of q alleles in the last generation that have given the same phenotype as the Q allele
  3. (1) : single nucleotide polymorphism
  4. (2) : microsatellite
  5. Mean square errors (MSEs) in cM2 of quantitative trait locus (QTL) location estimates obtained by the T2 and HAPim methods for various phenocopy rate values, t = 100, N = 400, and a marker spacing of 0.25 cM.
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BMC Genomics

ISSN: 1471-2164

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