. 2009 Mar 13;10:106. doi: 10.1186/1471-2164-10-106

Table 3.

The genotype frequencies in different scenarios in the presence of MCB or genotyping errors.

Scenarios

Missing Call Bias

Genotyping Errors for No-Calls

Scenario I

\begin{array}{l} p_{A A}^{o b s} = c p_{A A} / (c p_{A A} + p_{A a} + p_{a a}) \\ p_{A a}^{o b s} = p_{A a} / (c p_{A A} + p_{A a} + p_{a a}) \\ p_{a a}^{o b s} = p_{a a} / (c p_{A A} + p_{A a} + p_{a a}) \end{array}

\begin{array}{l} p_{A A}^{o b s} = c p_{A A} + c o n f (1 - c) p_{A A} \\ p_{A a}^{o b s} = p_{A a} + (1 - c o n f) (1 - c) p_{A A} \\ p_{a a}^{o b s} = p_{a a} \end{array}

Scenario II

\begin{array}{l} p_{A A}^{o b s} = p_{A A} / (p_{A A} + c p_{A a} + p_{a a}) \\ p_{A a}^{o b s} = c p_{A a} / (p_{A A} + c p_{A a} + p_{a a}) \\ p_{a a}^{o b s} = p_{a a} / (p_{A A} + c p_{A a} + p_{a a}) \end{array}

\begin{array}{l} p_{A A}^{o b s} = p_{A A} + (1 - c o n f) (1 - c) p_{A a} \\ p_{A a}^{o b s} = c p_{A a} + c o n f (1 - c) p_{A a} \\ p_{a a}^{o b s} = p_{a a} \end{array}

Scenario III

\begin{array}{l} p_{A A}^{o b s} = p_{A A} / (p_{A A} + c p_{A a} + p_{a a}) \\ p_{A a}^{o b s} = c p_{A a} / (p_{A A} + c p_{A a} + p_{a a}) \\ p_{a a}^{o b s} = p_{a a} / (p_{A A} + c p_{A a} + p_{a a}) \end{array}

\begin{array}{l} p_{A A}^{o b s} = p_{A A} \\ p_{A a}^{o b s} = c p_{A a} + c o n f (1 - c) p_{A a} \\ p_{a a}^{o b s} = p_{a a} + (1 - c o n f) (1 - c) p_{A a} \end{array}

Scenario IV

\begin{array}{l} p_{A A}^{o b s} = p_{A A} / (p_{A A} + p_{A a} + c p_{a a}) \\ p_{A a}^{o b s} = p_{A a} / (p_{A A} + p_{A a} + c p_{a a}) \\ p_{a a}^{o b s} = c p_{a a} / (p_{A A} + p_{A a} + c p_{a a}) \end{array}

\begin{array}{l} p_{A A}^{o b s} = p_{A A} \\ p_{A a}^{o b s} = p_{A a} + (1 - c o n f) (1 - c) p_{a a} \\ p_{a a}^{o b s} = c p_{a a} + c o n f (1 - c) p_{a a} \end{array}