Supplemental Material for Schlather et al., 2019
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
File S1: Additional method section on setting a target coverage.
File S2: Additional method section on the graphical representation of haplotype blocks.
File S3: Additional method section - toy example for calculation of bEHH.
File S4: Script to simulate a diallel design in MoBPS
Table S1: Proportion of variance explained between the full SNP-dataset (X), a SNP-subset (Xs) and the block dataset (Z). For comparability the number of parameters in Xs and Z were chosen equally using traditionally heritability estimation as in de los Campos (2017).
Table S2: Influence of the window size on the haplotype library for chromosome 1 in the KE DH-lines with a target coverage of 95%.
Table S3: Influence of the weighting of block length (wl) and number of haplotypes (wn) on the haplotype library for chromosome 1 in the KE DH-lines with a target coverage of 95%.
Table S4: Influence of using the extended-block-identification on the haplotype library in dependency of the parameter t of the extended-block-identification-step for chromosome 1 in the KE DH-lines with a target coverage of 95%.
Figure S1: Dataset for the toy example used in File S3.
Figure S2: Comparison of the block structure and a bifurcation plot (Sabeti et al., 2002, Gautier and Vitalis, 2012) according SNP 10,000 on chromosome 1 in the KE DH-lines.
Figure S3: Comparison of the block structure for MCMB=1000 (A), MCMB=5000 (B), MCMB=20,000 (C) for the first 20,000 SNPs of chromosome 1 in the KE DH-lines.