Polymorphism detection. (a) Comparison of Illumina reads and longer, dideoxy-sequenced, randomly cloned fragments (Sanger) with respect to how well they align to the reference genome. The distributions are very similar, except that longer reads that cannot be aligned are more likely to be anchored by a short stretch of presumably homologous sequence. (b) Average number of indels between the sequenced lines and the reference genome, divided into variants that are shorter and longer than the reference genome and shown as a function of the length of the variant. (c) Overlap between SNPs generated by this study and two previous resequencing studies,. (d) Characterization of new sequence identified by de novo assembly. (e) An example of a region containing new sequence. The graphs show sequence similarity (coding sequence in dark green, noncoding sequence in light green; yellow shows alignment) to the majority haplotype in Sweden, which contains a ~1-kb fragment of new sequence not found in the reference genome. The new fragment is also found in A. lyrata, indicating that it is ancestral; however, the region has been subject to several more rearrangements since the species diverged. The polymorphism may have functional consequences, as it affects putative coding sequence. (f) Distribution of large variants increasing length (blue; identified using de novo assembly), large variants decreasing length (green; inferred from sequencing coverage) and SNPs (synonymous nucleotide diversity, π black line) along chromosome 1. Chromosomes 2–5 show an analogous pattern ().