The domestic cow ( Bos taurus) is a ruminant that belongs to the Cetartiodactyl order of eutherian mammals. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of sequence and structural variants. CNV discovery was affected dramatically by platform resolution and coverage biases. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. For larger indels, a combination of split-read and read-pair approaches proved to be complementary in finding different signatures. Coding insertions and deletions (indels) were found to be enriched for size in multiples of 3 and were located near the N- and C-termini of proteins. The performance of resequencing SNP detection was assessed by combining SNPs that were identified to be either in identity by descent (IBD) or in copy number variation (CNV) with results from SNP array genotyping. We report the integration of the whole genome sequence of a single Holstein Friesian bull with data from single nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) array technologies to determine a comprehensive spectrum of genomic variation. This requires an accurate identification of the different types of variation in individual genomes. Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations.
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