Fig. 4

Correspondence between the ploidy predicted by the SCoPE approach and the normalized read depth coverage (RDC) along the entire chromosome sequences. The correspondence between the chromosomal ploidy and the normalized read depth coverage of chromosomes 16 (red box), 27 (blue box) and 31 (green box) of the T. cruzi Y strain is shown. a Chromosomal ploidy predicted by the SCoPE approach. b The blue line corresponds to the normalized RDC of each position, estimated by the ratio between the RDC and the genome coverage. Below, the protein-coding genes are depicted as rectangles drawn as proportional to their length, and their coding strand is indicated by their position above (top strand) or below (bottom strand) the central line. Cyan and black rectangles represent multigene families and hypothetical/housekeeping genes, respectively. Gaps are represented by gene-less regions with no read coverage. Chromosome 16 was predicted as disomic, 27 as trisomic and 31 as tetrasomic. The regions of low coverage correspond to regions rich in multigene families or chromosomal gap regions. c The predicted ploidy based on the proportion of the alleles in the heterozygous SNP positions for chromosomes 16, 27 and 31 is shown. The peak of 0.5 classifies chromosome 16 as diploid, the peaks of 0.3 and 0.6 classify chromosome 27 as triploid, and the peaks of 0.2-0.8 and 0.5 classify chromosome 31 as tetraploid