Determine the transgene location (within a specific chromosomal region)
Analyze the number of integration sites
Interrupted chromosomal regions can be identified in mice with unusual phenotypes.
The relationship between a transgene and specific genetic markers can be determined
The presence of homozygosity can be determined.
Determine the size and numbers of transgenes using high resolution fiber FISH when multi-copies are involved
Correlation studies between integration sites and the level of gene expression (detecting regions that shut off the transgene expression) can be performed.
 
Figure 2: Example of Insertion Mapping in a transgenic mouse chromosome.
References:
Dong S, Leung KKH, Pelling AL, et al.
Circling, deafness and yellow coat colour displayed by the chromosome 3 mouse mutant yellow submarine (Ysb) and light coat circling (Lcc).
Genomics 79(6):777-84 2002.
Nakajima H, Nakajima HO, Soonpaa MH, et al.
Heritable lympho-epithelial thymoma resulting from a transgene insertional mutation
Oncogene 19: 32-38 2000
Merrihew RV, Clay WC, Condreay JP, et al.
Chromosomal integration of transduced recombinant baculovirus DNA in mammalian cells
Journal of Virology 75 : (2) 903-909 JAN 2001
For more references, please check out the publications in the reliability section.