Genomic resequencing data in the northern bottlenose whale, Hyperoodon ampullatus

This dataset contains resequencing data used in our northern bottlenose whale genomics research. In this project, we analyzed population structure, demographic history, and signatures of selection. Source code for genomic analyses is available at github.com/edegreef/NBW-resequencing. Data uploaded here contain:


NBW_all_variantcalls.vcf.gz - All variant calls, including both indels and SNPs
NBW_SNPS_unfiltered.vcf.gz - Unfiltered SNPs
NBW_SNPS_filtered_population_analyses.vcf.gz - Filtered SNPs for population analyses. Filtered for quality (removed qual < 20, mq < 30, qd < 2, missingness > 0.4), biallelic sites, autosomes, removed structural variants, minor allele count 2, minimum scaffold length 50kb, and sites in Hardy-Weinberg Equilibrium
NBW_SNPS_filtered_pruned_population_analyses.vcf.gz - Additionally LD-pruned with r2 > 0.5
NBW_SNPS_filtered_demography_analyses.vcf.gz - Filtered SNPs for demography analyses. Filtered for quality, biallelic sites, autosomes, removed structural variants, minimum scaffold length 100kb, and sites in Hardy-Weinberg Equilibrium
NBW_SNPS_filtered_imputed_haplotype_analyses.vcf.gz - Filtered and imputed SNPs for haplotype analyses. Filtered for quality, biallelic sites, autosomes, removed structural variants, max-missingness 0.1, minor allele count 2, minimum scaffold length 50kb.
NBW_SNPS_filtered_Xchr.vcf.gz & NBW_SNPS_filtered_Ychr_males.vcf.gz - Filtered SNPs on X & Y chr. Filtered for quality, non-biallelic sites, removed structural variants, minor allele count 2, minimum scaffold length 50kb.