Overlay Plots (Malecot LD Map)

The Overlay Plots tab is shown below:

The Overlay Plots tab contains the following elements:

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

The M and L parameter estimates1M represents the youngest haplotype that is monophyletic. L represents the bias that occurs over large distances. See Maniatis et al. (2002) for more details. 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.