{"entity": "publication", "iuid": "725ec978bf1041179d2d8d62736f3184", "timestamp": "2026-08-20T20:26:38.609Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/725ec978bf1041179d2d8d62736f3184.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/725ec978bf1041179d2d8d62736f3184"}}, "title": "Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample.", "authors": [{"family": "Gilks", "given": "William P", "initials": "WP"}, {"family": "Pennell", "given": "Tanya M", "initials": "TM"}, {"family": "Flis", "given": "Ilona", "initials": "I"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Morrow", "given": "Edward H", "initials": "EH"}], "type": "journal article", "published": "2016-11-07", "journal": {"title": "F1000Res", "issn": "2046-1402", "volume": "5", "pages": "2644", "issn-l": "2046-1402"}, "abstract": "As part of a study into the molecular genetics of sexually dimorphic complex traits, we used high-throughput sequencing to obtain data on genomic variation in an outbred laboratory-adapted fruit fly ( Drosophila melanogaster) population. We successfully resequenced the whole genome of 220 hemiclonal females that were heterozygous for the same Berkeley reference line genome (BDGP6/dm6), and a unique haplotype from the outbred base population (LH M). 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 (Accession number SRP058502). We used Haplotype Caller to discover and genotype 1,726,931 small genomic variants (SNPs and indels, <200bp). Additionally we detected and genotyped 167 large structural variants (1-100Kb in size) using GenomeStrip/2.0. Sequence and genotype data are publicly-available at the corresponding NCBI databases: Short Read Archive, dbSNP and dbVar (BioProject PRJNA282591). We have also released the unfiltered genotype data, and the code and logs for data processing and summary statistics ( https://zenodo.org/communities/sussex_drosophila_sequencing/).", "doi": "10.12688/f1000research.9912.3", "pmid": "27928499", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5115224"}], "notes": [], "created": "2026-08-20T12:41:58.663Z", "modified": "2026-08-20T12:41:58.709Z"}