Data S1. Substitution and indel variant lists. (A) List of somatic substitution and indel variants in DFT1. Genotypes in each tumour are displayed as the number of reads supporting the mutation as a fraction of total reads covering the site. (B) List of somatic substitution and indel variants in DFT2. Notation is as described in (A). (C) List of somatic substitution and indel variants in 340T, the non-transmissible carcinoma. Notation is as described in (A). (D) List of germline substitutions and indels. List excludes variants falling into region of germline copy number polymorphism (Data S2). Notation is as described in (A). Data S2. Germline copy number polymorphisms. Genomic intervals with evidence of germline copy number polymorphism in the Tasmanian devil population. Bins occurring within these intervals were excluded from tumour copy number segmentation. Data S3. Copy number plots. Allele-specific copy number profiles for DFT1 and DFT2 tumours. Total copy number is represented in green, minor copy number is represented in blue. Data S4. Circos plots. Summary plots of absolute copy number profiles for DFT1 and DFT2 tumours, integrated with their respective structural variant genotypes. Total copy number profile is shown as a circular ring track, whereas rearrangements are displayed as arcs connecting chromosome regions in the centre.