D. melanogaster, line B52, mitochondrial DNA reads
DNA was extracted from pools of 50 adult female flies using Qiagen DNeasy Blood & Tissue kits. Samples were then sequenced to approximately 12x nuclear genomic depth at the Beijing Genomics Institute. Sequencing was performed on an Illumina HiSeq2000 using 100-bp paired-end reads with a 450–500 bp insert size. Raw reads were aligned to the D. melanogaster mitochondrial reference genome (RefSeq NC001709.1, r5.44) using Mosaik. Duplicate reads were removed with Picard. Bam files containing the aligned reads were then converted back into these fastq files with Picard.