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.