Variant Calls from Holstein Cattle with Recurrent Mastitis

Fifty Holstein cattle were whole-genome sequenced on the Illumina NovaSeq 6000 platform to investigate mastitis susceptibility. The dataset comprises 25 mastitis-susceptible cows and 25 healthy controls, with variant calls provided in VCF files. These files represent the minimal data required to reproduce genome-wide association study findings from the associated manuscript.

Use Cases

• Genome-wide association study (GWAS) for mastitis susceptibility based on case-control design.
• Identifying candidate SNPs associated with disease resistance in dairy cattle.
• Reproducing genomic analysis findings from the associated scientific manuscript.
• Comparative genomic analysis of Holstein populations using high-confidence variant data.

Strengths

• Includes a balanced case-control cohort of 50 animals, with 25 susceptible and 25 healthy cows.
• Data generation used the high-throughput Illumina NovaSeq 6000 sequencing platform.
• Variants underwent quality filtering to produce high-confidence SNPs for analysis.
• Raw sequencing data is archived in a public repository (EVA accession PRJEB88141).

Limitations

• The dataset provides only processed VCF files; raw sequencing reads are stored elsewhere.
• Column names and specific variant annotations within the VCF files are not detailed in the metadata.
• The dataset's scale is limited to 50 animals from a single breed.

Provenance

Source

Shiho Miyata

Collection Method

Whole genome resequencing and variant calling using standard bioinformatics pipelines.

Time Range

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Freshness

Last updated on 2026-03-22.

Geography

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