Alignments of HiSeq reads for Adineta vaga individuals L1-L11 to A. vaga mitochondrial contigs

Alignments of HiSeq reads for <i>A. vaga</i> individuals L1-L11 to <i>A. vaga </i>mitochondrial contigs in the BAM format. HiSeq reads for <i>A. vaga</i> individuals L1-L11 were aligned to the mitochondrial contig of the individual L4 used as a reference. Sequence of L4 mitochondral contig in the FASTA format is also uploaded (file 'L4.mito.contigs.fasta'). For individual L1 carrying a divergent mitochondrial haplotype, we also provide alignments of L1 HiSeq reads to L1 mitochondrial contigs (file 'L1.vs.L1.mito.contigs.bam'). L1 mitochondrial contigs were recovered from the L1 diploid assembly generated using MiSeq reads and can be found in the file 'L1.mito.contigs.fasta'. Alignments were obtained using Bowtie 2 (version 2.3.2) with the parameters “--no-mixed --no-discordant” specifying the maximum insert size of 800 base pairs with only a single best alignment of the pair of reads reported. BAM alignments were filtered to retain only properly paired reads with minimum MAPQ of 20.

本数据集包含*A. vaga*个体L1至L11的HiSeq测序读段与*A. vaga*线粒体重叠群（contig）的比对结果，格式为BAM格式（Binary Alignment Map）。本次比对以个体L4的线粒体重叠群作为参考序列，将所有L1至L11个体的HiSeq测序读段比对至该参考序列。L4个体线粒体重叠群的FASTA格式（FASTA format）序列文件亦已上传，文件名为`L4.mito.contigs.fasta`。针对携带高度分化线粒体单倍型的个体L1，本数据集额外提供了其HiSeq测序读段与自身线粒体重叠群的比对结果，对应文件为`L1.vs.L1.mito.contigs.bam`。L1个体的线粒体重叠群由基于MiSeq测序读段组装得到的L1二倍体基因组装配结果中提取获得，相关序列文件为`L1.mito.contigs.fasta`。所有比对均通过Bowtie 2（版本2.3.2）完成，参数设置为`--no-mixed --no-discordant`，指定最大插入片段长度为800碱基对，且仅输出读段对的唯一最优比对结果。后续对BAM格式的比对结果进行了过滤，仅保留配对正确且比对质量值（Mapping Quality, MAPQ）不低于20的读段对。