Missing call bias in high-throughput genotyping

Fu, Wenqing; Wang, Yi; Wang, Ying; Li, Rui; Lin, Rong; Jin, Li

doi:10.1186/1471-2164-10-106

Table 3 The genotype frequencies in different scenarios in the presence of MCB or genotyping errors.

From: Missing call bias in high-throughput genotyping

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

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