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Identification and annotation of genetic variants (SNP/Indel) in Danish Jutland cattle

Tuesday, August 19, 2014
Posters (The Westin Bayshore)
Ashutosh Das , Dept. Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
Frank Panitz , Dept. Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
Lars-Erik Holm , Dept. Molecular Biology and Genetics, Aarhus University, Tjele, Denmark
Abstract Text: We sequenced the whole-genome of a Danish Jutland bull to identify genetic variants (SNP/indel). Using UnifiedGenotyper from the Genome Analysis Toolkit (GATK), we identified 6,812,198 SNPs and 804,453 indels. There were 2,598,000 (38.1%) novel SNPs and 607,923(75.6%) novel indels while the remaining was annotated in dbSNP build 133. In-depth annotation of the variants revealed that 45,776 SNPs affected the coding sequences of 11,538 genes, 221 SNPs predicted to cause a premature stop codon, 17 to cause a gain in coding sequence and 20,828 predicted to be non-synonymous. We identified 1,122 indels in coding sequences, 832 predicted to cause frame shift, 89 predicted to be inframe insertion and 115 to be inframe deletion. We detected a higher level of genetic variation in the Jutland bull compared to similar data from Holstein cattle.

Keywords:

Cattle

whole-genome

SNP/indel

annotation

See more of: Posters: Methods and Tools - Genome Sequencing
See more of: Methods and Tools: Genome sequencing
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