PT - JOURNAL ARTICLE AU - William P. Gilks AU - Tanya M. Pennell AU - Ilona Flis AU - Matthew T. Webster AU - Edward H. Morrow TI - Whole genome resequencing of a laboratory-adapted <em>Drosophila melanogaster</em> population sample AID - 10.1101/081554 DP - 2016 Jan 01 TA - bioRxiv PG - 081554 4099 - http://biorxiv.org/content/early/2016/10/17/081554.short 4100 - http://biorxiv.org/content/early/2016/10/17/081554.full AB - As part of a study into the molecular genetics of sexually dimorphic complex traits, we used next-generation sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly (Drosophila melanogaster) population. We successfully resequenced the whole genome of 2 females from the Berkeley reference line (BDGP6/dm6), and 220 hemiclonal females that were heterozygous for the same reference line genome, and a unique haplotype from the outbred base population (LHM). The use of a static and known genetic background enabled us to obtain sequences from whole-genome phased haplotypes. We used a BWA-Picard-GATK pipeline for mapping sequence reads to the dm6 reference genome assembly, at a median depth-of coverage of 31X, and have made the resulting data publicly-available in the NCBI Short Read Archive (BioProject PRJNA282591). Haplotype Caller discovered and genotyped 1,726,931 genetic variants (SNPs and indels, &lt;200bp). Additionally, we used GenomeStrip/2.0 to discover and genotype 167 large structural variants (1-100Kb in size). Sequence data and quality-filtered genotype data are publicly-available at NCBI (Short Read Archive, dbSNP and dbVar). We have also released the unfiltered genotype data, and the code and logs for data processing, summary statistics, and graphs, via the research data repository, Zenodo, (https://zenodo.org/, ’Sussex Drosophila Sequencing’ community).