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Additional file 9: Figure S5. Sex assignment for the 1159 goats sampled in VarGoats. Representation of the ratio of read number between the autosomes and the X chromosome and the read number on the Y chromosome for each animal to determine its sex. The horizontal bar corresponds to the threshold of 25 reads from the Y scaffold allowing to differentiate males from females.

Additional file 2: Supplementary Fig. 1. Additional figures supporting the main text of the manuscript. Referred to as Supplementary Figs. 1–3. Supplementary Fig. 1. Volcano plot of differentially expressed genes (padj 1). Supplementary Fig. 2. Outliers detected by sample clustering (WGCNA). Supplementary Fig. 3. Principal component analysis of herd effect. A) with herd effect, B) herd effect removed.

Additional file 6: Figure S4. Tranche plot produced by VariantRecalibrator for SNPs. Description: Partition of the call sets into quality tranches. The tranches correspond to certain levels of sensitivity relative to the truth sets (the highest tranche corresponds to a high accuracy call set but with the lowest value of sensitivity).

Additional file 3: Figure S1. Distribution of the concordance rates. Concordance rates (CR) between sequence variants and 50 k genotypes for 457 individuals. The figure shows a clear disruption in the distribution of CR, thus we found it easy and relevant to discard the samples below a concordance rate of 70% between sequence and chip SNP data.

Additional file 5: Figure S3. Pairwise comparisons of the annotations chosen in VQSR for InDels. Description: Modeling report generated by GATK VariantRecalibrator for every pairwise combination of annotations used (QD, DP, FS, MQRankSum, ReadPosRankSum and SOR), with a 2D projection of the Gaussian mixture model.

BACKGROUND Since their domestication 10,500��years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. FINDINGS A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. CONCLUSIONS We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies.