Data from: Structural and epistatic regulatory variants cause hallmark white spotting in cattle
Data files
Oct 08, 2025 version files 1.96 GB
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README.md
2.02 KB
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speckled_phenos.txt
2.10 KB
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speckling_GWAS_geno_set.bed
1.28 GB
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speckling_GWAS_geno_set.bim
679.70 MB
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speckling_GWAS_geno_set.fam
3.76 KB
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splotchy_GWAS_geno_set.bed
1.33 MB
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splotchy_GWAS_geno_set.bim
1.25 MB
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splotchy_GWAS_geno_set.fam
1.94 KB
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splotchy_phenos.txt
1.06 KB
Abstract
Genotype and phenotype data underlying analyses presented in the manuscript "Structural and epistatic regulatory variants cause hallmark white spotting in cattle". This package contains data required to recreate analyses presented in that paper, specifically genome wide association analyses of the 'splotchy' and 'speckly' coat pattern phenotypes.
Dataset DOI: 10.5061/dryad.fxpnvx15q
Description of the data and file structure
Two filesets are included in this package, representing the genotypes and phenotypes used for 'Splotchy face' and 'Speckly coat' genome-wide association analyses. Both filesets consist of Plink binary format files (.bed, .bim, .fam) and a phenotype file, also directly loadable using Plink software.
Splotchy face dataset:
splotchy_phenos.txt
splotchy_GWAS_geno_set.bed
splotchy_GWAS_geno_set.bim
splotchy_GWAS_geno_set.fam
Speckly coat dataset:
speckled_phenos.txt
speckling_GWAS_geno_set.bed
speckling_GWAS_geno_set.bim
speckling_GWAS_geno_set.fam
Files and variables
File: speckling_GWAS_geno_set.bed
Description: Plink format binary file for genome-wide genotypes for Speckly association analysis
File: speckling_GWAS_geno_set.fam
Description: Plink format animal ID file for Speckly association analysis
File: speckled_phenos.txt
Description: Phenotype for Speckly association analysis
Variables
- FID: Family ID
- IID: Individual ID
- speckles_on_coat: Phenotypic class
File: speckling_GWAS_geno_set.bim
Description: Plink format variant ID file for Speckly association analysis
File: splotchy_phenos.txt
Description: Phenotype for Speckly association analysis
Variables
- FID: Family ID
- IID: Individual ID
- Splotchy: Phenotypic class
File: splotchy_GWAS_geno_set.fam
Description: Plink format animal ID file for Splotchy face association analysis
File: splotchy_GWAS_geno_set.bim
Description: Plink format variant ID file for Splotchy face association analysis
File: splotchy_GWAS_geno_set.bed
Description: Plink format binary file for genome-wide genotypes for Splotchy face association analysis
Code/software
Plink software, various current and older versions