Fig. 1.

Example genomes before and after segmental deletion and duplication. Top images are the reference genome while bottom images are the genome after deletion/duplication. Each colored box represents a single base pair and base pairs between two vertical orange lines represent segments. The letters below a base pair identify the position of that base pair in the reference genome. Assume this is example holds for any single chromosome labeled z. (a) Shows a deletion of segment 2 (base pairs B through C) producing structural variant ]z: A],[z: D[. The copy number of each of the mated breakpoints ($c_{]\mathtt{z}:\mathtt{A}]}$ and $c_{[\mathtt{z}:\mathtt{D}[}$) and the copy number of each of the segments containing these breakpoints (${\gamma }_{]\mathtt{z}:\mathtt{A}]}$ and ${\gamma }_{[\mathtt{z}:\mathtt{D}[}$) are all 1 ($c_{]\mathtt{z}:\mathtt{A}]}=c_{[\mathtt{z}:\mathtt{D}[}={\gamma }_{]\mathtt{z}:\mathtt{A}]}={\gamma }_{[\mathtt{z}:\mathtt{D}[}=1$). (b) Shows a duplication of segment 2 producing structural variant [z: B[,]z: C]. The copy number of each of the mated breakpoints is 1 ($c_{[\mathtt{z}:\mathtt{B}[}=c_{]\mathtt{z}:\mathtt{C}]}=1$) while the copy number of each of the segments containing breakpoints is 2 (${\gamma }_{[\mathtt{z}:\mathtt{B}[}={\gamma }_{]\mathtt{z}:\mathtt{C}]}=2$)