Analysis of the marker data is a four part process:-

1) marker segregation patterns are entered

2) All possible pairwise combinations of markers are then analysed. For each pair of markers, a LOD (log-odds) score and Ø (theta) value are calculated. The LOD score reflects how confident one can be that the markers are linked, and the Ø value is a measure of the distance between the markers. Both values reflect the degree of co-segregation between those two markers (basically, how similar are their band-patterns when typed on the same mapping panel). Two markers with very similar patterns have high a LOD and low Ø (they are definitely linked and are close together); markers with dissimilar patterns have the reverse.

3) Markers are sorted into ‘linkage groups’ - clusters of markers in which each marker is linked to at least one other in the group by a LOD score above a given threshold. For a map involving N markers, the threshold is generally set at log(N^2) to avoid the risk of “false” or fluke links. For 1000 markers, therefore, the threshold is 6.

Ideally, all the markers on a given chromosome will fall into a single linkage group.

4) The table of pairwise LOD and Ø values for all markers in a linkage group are then passed to the mapping programme (How do you make a map from the links?).