Fig. 2

Schematic representation of genome chunking workflow. a A step-by-step procedure involved in creating 630 chunks from a genome. b Generation of chunks by setting cut points, and practical steps involved in creating chunks from a given chromosome length. The entire genome is divided into 5 Mb segments (n = 630) by making virtual cuts. Next, a 2.5 Mb distance is added to both ends of the initial cut point to determine the presence of functional sites and to allow Haploview interval analysis among intergenic regions. c Haploview analysis: The three distinctive regions, marked 1, 2, and 3 are the new cut points of a chunk selected by Haploview analysis to identify the relationships among the selected SNPs. We recalculated the length of each cut point to include related biological information to obtain informative chunks (as denoted by 20_6_7_hap.LD.PNG, 20_7_8_hap.LD.PNG, and 20_8_9_hap.LD.PNG, respectively). These regions represent a precise sequence information ranging from 4 to 6 Mb in length, which could be information related to CNV or genes. d Distribution of chunks. The graph illustrates the distribution of functionally related chunks along with functionally unrelated chunks and the classification of chunks based on their respective numbers of markers