Figure 1.

Different types of TE insertions and TE genotypes. (A-C) Three different types of TE insertions with light yellow boxes indicating the time frames for when each arises. The colored triangles point to the origin of chromosomes carrying insertions. (A) Germline TE insertions are inherited from parents, and thus are present in every cell of the body. (B) De novo TE insertions arise during gametogenesis of the parents or early embryogenesis of the child, and thus are not detected in blood samples of the parents. (C) Somatic insertions occur during development and aging and create genetic mosaicism in an individual. Depending on when and where insertions occur, they are detected in different tissues at different mosaic levels. (D) Every TE insertion in an individual genome has three genotypes: homozygous (1/1), heterozygous (0/1), or no insertion (0/0). A homozygous insertion produces TE-junction-spanning reads originating from two insertion alleles; a heterozygous insertion produces reads from both insertion and reference alleles. Chromosomes carrying a non-reference TE insertion and sequence reads derived from the chromosomes are marked in red.