Some cautions

• Never guess: it is always better to having missing data (scored as 0 in the previous example) than data points which are wrong. Wrong data may be interpreted as indicating a  recombination(s) when there wasn't one.
• Mapping can only tell you the most likely order of markers, given the data. This can often change given new data, and there are a number of things that can result in wrong conclusions. Genetic maps are only “best guess”.
• Very distant markers are difficult to associate because their co-segregation is not much different from random association.
• Very close markers are difficult to order because there is little data which differentiates between orders. It is important to validate the small amount of data from which close linkage between a pair of markers is established.