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

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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
Original languageEnglish
Publication year17 Aug 2014
Number of pages3
Publication statusPublished - 17 Aug 2014
Event10th World Congress on Genetics Applied to Livestock Production (WCGALP) - The Westin Bayshore, 1601 Bayshore Drive, Vancouver, BC V6G 2V4, Vancouver, Canada
Duration: 17 Aug 201422 Aug 2014
Conference number: 10th

Conference

Conference10th World Congress on Genetics Applied to Livestock Production (WCGALP)
Number10th
LocationThe Westin Bayshore, 1601 Bayshore Drive, Vancouver, BC V6G 2V4
CountryCanada
CityVancouver
Period17/08/201422/08/2014

    Research areas

  • Cattle, whole-genome SNP, indel annotation

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