Duplicated regions of T. c. marinkellei and T. c. cruzi Sylvio X10 inferred from short reads. Short read coverage on assembly scaffolds of T. c. marinkellei B7 and T. c. cruzi Sylvio X10. Coverage was counted in 100 bp sliding windows along the scaffolds, with 50 bp step size. Each dot represents a 100 bp window. The horizontal axis shows the position of the window along the scaffold and the vertical axis shows the log10-scaled coverage of each window. Coverage was incremented by 1 to avoid infinite values for empty regions. Red lines show the global median coverage and blue lines show +/− 2X of the median absolute deviation. On scaffold 1093 (Tcm) the amplified region contained a dynein light chain protein, a nucleoside transporter and two genes of unknown function. On scaffold 1101 the first amplified region was 3 kb and contained a gene of unknown function, the second region was 3.7 kb and contained a pyruvate phosphate dikinase gene, the third region was 1.2 kb and contained a gene of unknown function. Scaffold 1531 (Tcc X10) contained a 4.7 kb amplification which contained a nucleoside transporter. Scaffold 1556 (Tcc X10) contained two genes of unknown function. Scaffold 3025 (Tcc X10) contained a 5 kb amplification with a copper-transporting ATPase gene. Scaffold 78 from Tcm showed evidence of aneuploidy, as the mean coverage was lower than for the other scaffolds.