Table 4.

The bisulfite conversion model

	Epigenotype g
Z	C	G	A	T	$\stackrel{\text{me}}{\mathsf{C}}$	$\underset{\text{me}}{\mathsf{G}}$
C	$\widehat{\rho }\alpha$	0	0	0	$1-\widehat{\rho }\beta$	0
G	0	ρ α	0	0	0	1−ρ β
A	0	1−ρ α	1	0	0	ρ β
T	$1-\widehat{\rho }\alpha$	0	0	1	$\widehat{\rho }\beta$	0

The probability P(Z=z∣g,r) of Z given the epigenotype g and the strand r. Here α is the rate of failed bisulfite conversion and β is the rate of inappropriately converted nucleotides. The parameter ρ is 0 if r=fwd, 1 if r=rev, and $\widehat{\rho }=1-\rho$. For example, P(Z=C∣g=C,r=fwd)=α