1 - MBCDPv2.9 2 - ARS1.2 MBCDPv2.9 .bam by mixed groups 3 - ARS1.2 MBCDPv2.9 .bam by breed

14x WGS of MBCDPv2.9

Public access to these data (.bam files) is available for use with a desktop version of IGV.   

ARS-UCD1.2 .bam file URLs by Breed or Mixed groups of 8

These USMARC WGS reads were mapped to the ARS-UCD1.2 bovine genome assembly of Hereford female L1 Dominette 01449 as part of a previous 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 are available as part of BioProject PRJNA324822.  

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.

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.

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