Figure 6.

Examples of sequence alignments of contig fragments containing DownCNV/PAVs. The sequence of the barley cultivar Morex is shown at the top and the sequence of cultivar Barke at the bottom. (A) Schematic representation of how an insertion in Barke can lead to a DownCNV/PAV call. Sequence regions that are orthologous are connected by shaded areas. The additional sequence in Barke is depicted in light blue. The full contig fragment is composed of 10 overlapping probes. Those probes which overlap the breakpoint of the insertion will produce a low intensity signals or no signals, resulting in a reduced overall signal of the targeted contig fragment. (B) Contig fragments with multiple insertions/deletions. (C) Contig fragment with multiple deletions, including one that expands past the border of the fragment. (D) Contig fragment that contains additional sequences in Barke. (E) Contig fragment that contains an insertion/deletion that most likely originates from template slippage. The numbers in circles identify different types of insertions/deletions: 1, insertion/deletion that contains no obvious signature; 2, insertion/deletion that shows a typical signature of double-strand break repair via single-strand annealing (SSA); 3, insertion/deletion which contains filler sequence (indicated by a curly bracket) and that presumably is the result of DSB repair via synthesis-dependent strand annealing (SDSA); 4, insertion/deletion originated from template slippage of direct repeats (indicated by arrows).