Figure 1.

Read mapping to the reference genome provides evidence for integration and excision, illustrated for the case of one mobile genetic element (MGE). The central region of the integrated sequence of Yucahu-i (between black bars) has been deleted to focus on details of reads mapped to the start and end of the region. Read sequences that match the genome sequences are shown as gray bars; small vertical colored bars adjacent to read portions in agreement with the reference indicate bases that disagree with the reference. The yellow, purple, blue, green, and orange arrows indicate distinct nucleotide sequences (same color, same sequence). In the panel demonstrating that some cells that lack the integrated MGE, one read has been split (the black line links the two parts of a single read) to illustrate agreement with the flanking sequence at both ends of the integrated region. Note that the sequence designated by the purple arrow occurs twice when the MGE is integrated. The vertical colored bars indicate single-nucleotide polymorphisms (SNPs) relative to the reference genome sequence and thus do not represent the sequence itself.