Fig. 2

Flowchart of the main computational steps in the findZX/findZX-synteny pipeline (A), and miniatures of the five output plot types (B-F). A The flowchart boxes in blue are common for both findZX and findZX-synteny. The green boxes are specific for findZX and orange boxes are specific for findZX-synteny. Parallelograms (top row) represent input data, and rectangles represent computational steps and output. See Main text and Supplementary Methods (Additional File 1) for details. Plot type 1 (B; see also Fig. 3) and 2 (C; see also Supplementary Fig. 2, Additional File 1) show genome-wide heterozygosity and genome coverage values based on means across genome windows (here 1 Mb). Plot type 1 (B) shows sex differences and 2 (C) shows values for each sex separately. Plot type 3 (D; see also Fig. 4) shows heterozygosity and genome coverage values for each chromosome/scaffold, as well as chromosome/scaffold length. Plot type 4 (E; see also Fig. 5) shows mean ± SD sex differences (calculated from genome windows, here 1 Mb) for each chromosome/scaffold. Here we invoked the option to highlight certain chromosomes/scaffolds (specified in the configuration file; see Main text). Plot type 5 (F; see also Supplementary Fig. 3 and 4, Additional File 1) shows heterozygosity and genome coverage profiles for each studied individual and can be used to confirm that samples have been correctly sexed