Southern sea otter genotypes
datasetposted on 22.06.2019 by Annabel Beichman
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
This directory contains the filtered genotypes from southern sea otter (Enhydra lutris nereis) sequencing reads (Project number: PRJNA472597, Acc. SRR8597300) mapped to the domestic ferret reference genome (GCF_000215625.1). The files are in vcf format, and the genome was split into 323 chunks to reduce file sizes. Each of the first 1-224 .vcf files contain a single scaffold, and the remaining 225-323 vcf files each contain groups of 76 smaller scaffolds. The directory ferret_genome_interval_bedfiles.tar.gz contains the bed files that give the scaffold coordinates of each .vcf file (e.g. interval_244.bed gives the coordinates of the scaffolds contained in the vcf file labeled as 244: *.raw_variants.244.*.HQsites.Only.rmDotGenotypes.rmBadVars.vcf.gz). The reads were mapped, genotypes were called and filtered as described in the README and SI Methods in Beichman et al. 2019.