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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » WGS » MECDPv1.0
1 - MECDPv1.0
2 - ARS1.2 MECDPV1.0 .bam by breed

14x WGS of MECDPv1.0

Notice:  access to these data (.bam files) aligned to the ARS1.2 reference genomes is being migrated to a new system for use with a desktop version of IGV.   

ARS-UCD1.2 .bam file URLs by Breed (in progress)

/ARSUserFiles/30400500/CattleandSheepGenomicData/USMARC_Cattle46Breeds12.jpg

These USMARC WGS reads are mapped to the ARS-UCD1.2 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. 

The WGS of animals from the 27 additional breeds are currently in progress and access will be made available first at this site via IGV.  As data sets are validated for identity and quality, the FASTQ files will be deposited in the SRA at NCBI and be available as part of BioProject PRJNA324822. 

This citation describes the process:  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)

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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