Overlay Plots (Malecot LD Map)

The Overlay Plots tab is shown below:

The Overlay Plots tab contains the following elements:

•	A plot of the M and L parameter estimates over physical regions for each BY group.

The M and L parameter estimates¹ are used, along with an estimate of the LD measure Rho (calculated using the Linkage Disequilibrium analytical procedure) to fit the Malecot model Rho = (1-L)*M*exp(-E_i*d_i)+L to each interval of length d_i kb between consecutive SNPs via nonlinear optimization routines. Distances between pairs of SNPs can then be represented in terms of LD units (LDU), which are computed by summing (E_i*d_i) over all intervals between the pair of SNPs, and are shown on the Bivariate Plots (Malecot LD Map) tab.

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1

M represents the youngest haplotype that is monophyletic. L represents the bias that occurs over large distances. See Maniatis et al. (2002) for more details.