Mapping structural variants using the paired end read strategy. (a) A region of genome containing a translocation junction between two different chromosomes (red and blue). (b) The entire genome is fragmented, and fragments of a desired size, typically 500 bp, are selected. (c) The ends of the fragments are sequenced for a small fraction of the fragment length, typically 35 bp (black arrows). The Stephens et al.  study used 500 bp fragments and 37 bp sequencing reads but other combinations are possible. For variations, see . (d) The paired sequence tags are mapped back to the reference genome. Most pairs map back about 500 bp from each other on the same chromosome, but (e) the read pair spanning the translocation breakpoint maps back to two different chromosomes in the reference genome.