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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » WGS » MBCDPv2.9

14x WGS of MBCDPv2.9

View in IGV* by bull/breed or mixed groups of 8

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These USMARC WGS reads are mapped to the UMD3.1 bovine genome assembly of Hereford female L1 Dominette 01449 as part of a USDA ARS Specific Cooperative Agreement with Intrepid Bioinformatics in collaboration with the University of Louisville

Citation: Heaton MP, Smith TPL, Carnahan JK, Basnayake V, Qiu J, Simpson B, Kalbfleisch TS. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with high-altitude pulmonary hypertension. F1000Research 2016, 5:2003 (doi: 10.12688/f1000research.9254.1)

The FASTQ files have been deposited in the SRA at NCBI and be available as part of BioProject PRJNA324822.  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.

The purpose of this beef cattle diversity panel was SNP discovery and allele frequency estimation. To maximize the total number of unshared haploid genomes, sires within and between breeds were selected for pedigrees with minimal relationships. On the basis of the number of registered progeny, the breeds in this panel comprised greater than 99% of the germplasm used in the US beef cattle industry circa 2000. The group is estimated to contain more than 187 unshared haploid genomes and was expected to allow a 95% probability of detecting any allele with a frequency greater than 0.016 in the group.

 *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.