Supporting Information for Collaborative Cross Consortium, 2012

Supporting Information

• Supporting Information - Figure S1-S10 and Tables S1-S6 (PDF, 2.7 MB)
• Figure S1 - Intensity based haplotype assignment (PDF, 258 KB)
• Figure S2 - Distribution of shared recombination events before and after identifying related samples (PDF, 163 KB)
• Figure S3 - Breeding Performance in the extant CC-UNC population (PDF, 253 KB)
• Figure S4 - Heterozygosity in the autosomes CC lines (PDF, 63 KB)
• Figure S5 - Subspecific origin in the CC population (PDF, 188 KB)
• Figure S6 - LD decay in the CC (PDF, 182 KB)
• Figure S7 - Gametic disequilibrium in the CC and in the panel of 88 inbred strains (PDF, 368 KB)
• Figure S8 - Linkage and gametic disequilibrium in the 350 independent CC lines (PDF, 943 KB)
• Figure S9 - Recombination in the CC lines (PDF, 65 KB)
• Figure S10 - Founder contribution in each of the 350 CC lines (PDF, 62 KB)
• Table S3 - Number of lines genotyped in each CC population (PDF, 39 KB)
• Table S4 - Expected representation of founder strains on Chr X based on the funnel code (Figure 1) in the CC-UNC and CC-GND populations (PDF, 34 KB)
• Table S5 - Ancestral haplotype diversity in the CC (PDF, 31 KB)
• Table S6 - CC-UNC External Advisory Board (PDF, 48 KB)
• Table S1 - The table provides the MUGA genotypes for 458 CC lines and the eight founder strains, including SNP ID, chromosome and position on mouse build 37 (.zip, 8.6 MB)
• Table S2 - The table provides the following information for 458 CC samples used in this study: sample name, population, funnel code, percent contribution from each founder (using the single letter code, see Figure 1), heterozygosity, identity of missing founders, identity of overrepresented founders and the number of recombinations. (.zip, 17 KB)