Alignment of sequencing reads to yeast genomic sequence. (A) Sequence of Ty3 integration joint. High-throughput sequencing reads began with 17 nt from the U5 end of the Ty3 LTR and continued into genomic sequence. Informative reads aligned uniquely with ∼19 nt of target site DNA in the reference genome. Each unique junction defined an integration event. A sequencing read representing a collection of events at tK(CUU)F is shown. (B) Analysis of target loci. Reads captured by events separated by 10 nt or less were combined into clusters (shaded box). The distribution of reads (hits) among events clustered at tK(CUU)F is shown. (Dashed lines) Ty3 LTR sequences. Depending on the orientation in which Ty3 integrated, sequencing reads aligned with either the Watson or Crick strand of the genomic sequence of yeast reference strain S288C. (Right column) The numbers of reads for the same integration joint (event densities). The most-sequenced junctions in the two strands were offset by the 5-bp stagger characteristic of Ty3 insertion sites (triangles).
