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Genetic distances measured with recombination rates are approximately additive: if the distance from gene A to gene B is 15 m.u. and the distance from gene B to gene C is 20 m.u., the distance from gene A to gene C is 35 m.u. A female mouse is heterozygous for the three linked genes described.
Consider three genes L, R, and Q. You want to measure the map distance between these genes. You have at your disposal a dominant and a recessive allele for each of these genes, which you use to perform a three-point cross.
We generate these markers as the local maxima of the distance function to the background. Given the typical size of the nuclei, we pass min_distance=7 so that local maxima and, hence, markers will lie at least 7 pixels away from one another.
The mapper and mapping positions store all positions in Python coordinates, i.e. 0-based. Many users are working with data that is 1-based, such as GenBank or HGVS. Each map position type has a “to_hgvs” and “to_genbank” method for easy conversion.
Mitotic recombination is crossing over between homologous chromosomes during mitosis in somatic cells. Mitotic recombination is one explanation for a blue patch.
By doing this type of analysis with more and more genes (e.g., adding in genes D, E, and F and figuring out their relationships to A, B, and C) we can build up linkage maps of entire chromosomes. In linkage maps, you may see distances expressed as centimorgans or map units rather than recombination frequencies.
As shown in Figure 13.4, by using recombination frequency to predict genetic distance, the relative order of genes on chromosome 2 could be inferred. The values shown represent map distances in centimorgans (cM), which correspond to recombination frequencies (in percent).
