Genomic libraries are constructed from fragmented DNA and subcloned into circular vectors such as BACs or fosmids. The ends of these fragment inserts are directly sequenced from universal vector primers near the subcloning site (arrows) and are termed end-sequence pairs or paired-end sequences. End-sequence pairs are mapped to their best location in the human reference genome sequence assembly. End-sequence pairs that are discordant in terms of length (> 3 s.d. from the mean insert length) and/or orientation when mapped against the reference genome assembly may be indicative of deletions, insertions or inversion, as indicated (red, blue and green, respectively). End-sequence pairs consistent in terms of length and orientation are shown as grey.

a, Genomic clone libraries are constructed from different human DNA samples (Yoruban Nigerian samples NA18517 and NA18507). b, The inserts of ~1 million fosmid clones are end-sequenced for each individual and aligned against the reference human genome. This provides a tiling path for each individual's genome against the reference sequence. The amount of DNA sequence between the ends of a clone (between end-sequence pairs) is known approximately, even before the clones are sequenced. The end sequences of each clone are mapped to the reference sequence. If they map to sites that are farther apart in the reference sequence than in the test sequence clone, there is a deletion in the test sequence, relative to the reference sequence. Conversely, if the end sequences map to sites that are closer in the reference sequence than in the test sequence, there is an insertion in the test sequence. Overlapping clones refine the location of the insertion or deletion (dashed lines), in this case, near the CYP2D6 gene. c, Sequencing of the corresponding clone provides sequence-based resolution of the insertion or deletion and allows genotyping assays to be developed to type a large number of individuals.