Average call rate and >5%MAF SNPs for the cluster file breeds.

<p>For each breed used for the chip validation and cluster file definition, the number of samples, the number of >5%MAF SNPs and the average call rate are indicated.</p

SNPs by category in final design.

<p>The number of selected SNPs is indicated for each of the following categories. 1: SNP detected in an EST. 2: two alleles detected in the five considered breeds. 3: two alleles detected in Alpine and Saanen and Creole and (Boer or Savanna). 4: two alleles detected in two of the three milk and mixed breeds (Alpine, Saanen, Creole) and in Boer and Savanna. 5: two alleles detected in Alpine and Saanen and Creole. 6: two alleles detected in three out of the five breeds. 10: two alleles detected in each of the two milk breeds (Saanen and Alpine). 11: two alleles detected in one milk breed (Saanen or Alpine) and one meat breed (Creole or Boer or Katjang/Savanna). 12: two alleles detected in at least two meat breeds (Creole and Boer or Katjang/Savanna). 13: two alleles detected in one milk breed (Saanen or Alpine).</p

SNP identified in the five breeds or breed pool and in ESTs.

<p>The number on the diagonal is the number of SNPs found in a breed (Alpine, Boer, Creole, Saanen), breed pool (Katjang/Savanna) or in ESTs. Off diagonals are the number of SNPs shared between the two respective breeds.</p

Goat Genome scaffolds assembly.

<p>The goat genome scaffolds were sorted by decreasing size (x-axis) and the cumulative proportion of the assembled genome was plotted on the y-axis for all the scaffolds. The vertical line shows that >10kb scaffolds represent 97.2% of the assembled goat genome.</p

SNP spacing on the goat scaffolds.

<p>Spacing between the selected SNPs was calculated and the percentage of gaps (total number of gaps is 59,030 on goat scaffolds and 62,693 on UMD3.1 cattle assembly) is shown (y-axis) in each 5kb class ranging from 5 to 150kb (x-axis).</p

Distribution of estimated MAFs of the selected SNPs.

<p>The MAF for all the 60,000 selected SNPs was estimated based on the read counts for the two alleles.</p