# =============================================================== # Data files and information for the paper: Genome data from a 16th century pig illuminate modern breed relationships O. Ramírez, W. Burgos-Paz, E. Casas, M. Ballester, E. Bianco, I. Olalde, V. Novella, M. Gut, C. Lalueza-Fox, M. Saña, M. Pérez-Enciso 2014, Heredity ================== 60K SNP DATA ================== These files combine the information from American village pigs from Burgos et al. 2013 (doi: 10.1038/hdy.2012.109) and Near East samples from Manunza et al. 2013 (doi: 10.1371/journal.pone.0055891) FILES 4090_SNPs.ped and 4090_SNPs.map: These files (plink format) contain information about genotypes of 4090 SNPs in 434 individuals including the ancient sample. FILE Info.Samples.txt: This file contains the information about breed and country of samples analyzed. ============== SEQUENCE DATA ============== FILES Sequence.ped and Sequence.map: These files contains information about genotypes of 808858 SNPs extracted from 9 individuals, including the ancient sample. ANES1799 Ancient Spain CRGU1508 Creole Guatemala DU23M02_Duroc Duroc HA20U01_Hampshire Hampshire IBGM0327 Iberian Spain LR24F01 Landrace LW22F02 Large White PI21F06 Pietrain WBES0717 Wild boar Spain ================ ADMIXTURE INFO ================ FILE Admixture_12_k.Q file: This file contains the results of K=12 ancestry groups estimated with ADMIXTURE (Alexander et al. 2009) using the information of 4090 SNPs (Figure 2) =================== ALIGNED MT SEQUENCE =================== FILE mt.20130503.nohet.fas : aligned complete mt sequences used to draw figures 1 and S6 ================= RAW SEQUENCE DATA ================= Bam files for new samples and complete three raw data for the ancient sample are deposited in SRA http://www.ncbi.nlm.nih.gov/bioproject/255085 SubmissionID: SUB596929 BioProject ID: PRJNA255085 Accession: SRP044261 Organism name/label: Sus scrofa Title: Ancient and modern Sus scrofa Genome sequencing Accessions are ANES1799: SRR1509537 (SE raw data), SRR1509538 (BAM file) CRGU1508: SRR1513309 (BAM file) IBGM0327: SRR1513307 (BAM file) WBES0717: SRR1513306 (BAM file) For additional information, please contact: miguel.perez@uab.es # ======================================================================#