. Author manuscript; available in PMC: 2014 Dec 23.

Published in final edited form as: Zhejiang Daxue Xue Bao Nong Ye Yu Sheng Ming Ke Xue Ban. 2014;40(4):387–396.

Table 5.

Simulation result on estimation of recombination rate between three markers on two chromosome with known order, linkage phases, and r value

Marker

Segregation type

True value of r

Linkage phase

r̂

LOD score

\bar{\hat{r}}

M₁

M₂

ab×cd

0.100

c×c

0.125

54.960

0.112 ± 0.005

r×r

0.500

54.960

c×r

0.500

0.000

r×c

0.500

0.000

M₁

M₃

ab×cd

0.500

c×c

0.500

0.590

0.500±0.000

r×r

0.423

0.590

c×r

0.500

0.054

r×c

0.488

0.054

M₂

M₃

ab×cd

0.500

c×c

0.500

0.048

0.500±0.000

r×r

0.465

0.048

c×r

0.483

0.326

r×c

0.500

0.326

r: Recombination rate; r̂: Estimate of r; $\bar{\hat{r}}$ : The average of 100 estimate of r.

c: Coupling in the paternal parent and uninformative in the maternal parent, or vice versa; r: Repulsion in the paternal parent and uninformative in the maternal parent, or vice versa; c×c: Coupling in both parents; r×r: Repulsion in both parents; c×r or r×c: Coupling in the maternal parent and repulsion in the paternal parent, or vice versa.