17x WGS of MSDPv2.4
Reads mapped to Oar_v3.1 ovine genome assembly of a USMARC Texel ram (200118011) and a Danish Texel ewe
These USMARC WGS data were from an ARS Specific Cooperative Agreement with Intrepid Bioinformatics in collaboration with the University of Louisville. The purpose of this sheep diversity panel was SNP discovery and allele frequency estimation. The current version of this panel consists of 95 rams from nine breeds and the composite population, plus one Navajo-Churro ram with a rare ARK prion haplotype. The composite population (USMARCIII) consists of: 1/2 Columbia, 1/4 Hampshire, and 1/4 Suffolk).
The nine pure breeds were selected to represent genetic diversity for traits such as fertility, prolificacy, maternal ability, growth rate, carcass leanness, wool quality, mature weight, and longevity. The rams sampled from each breed were chosen to minimize genetic relationships among rams within breed.
Validated FASTQ file sets, producing genotypes concordant with those from 168 reference SNPs, have been uploaded to the SRA at NCBI, and are available as part of BioProject PRJNA324837. A manuscript describing these results entitled, "Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity," has been published at F1000Research. Additional access to the BAM files is provided by Intrepid Bioinformatics. These files can be loaded to the UCSC Genome Browser, downloaded (~30GB each), or dragged and dropped into other applications.
*Integrated Genome viewer will automatically load from Intrepid Bioinformatics when a Java Runtime Environment is present. Thus, a local Java installation is required. Mention of trade names or commercial products in this public information release is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.