Table 2 Number of single-end reads of mono-nucleosome cores isolated from MNase-digested DNA samples. Alignment to the genome was performed using ELAND using default parameters. The genome coverage was estimated as the number of uniquely mapped reads multiplied by the length of mono-nucleosomes (147 bp) divided by the sequenced medaka genome size (700 M bp). Since single-end short reads of length 25 nt were collected from MNase fragments, the accurate length of individual fragment could not be estimated. To have an approximate picture of the distribution of fragments obtained from MNase digestion, 32 arbitrary fragments were inserted into a standard plasmid vector and sequenced using Sanger sequencing. Of 24 sequences that could be anchored to unique positions, the average length was 150.2 nt with a standard deviation of 9.3 nt. If we use the actual fragment lengths in place of the ideal length (147 nt), the coverage would increase by ~2 %. The cumulative ratio of nucleotides covered by ≥ x (=1,2, …, 30) nucleosome core reads are shown in Additional file 1: Figure S1d, which indicates >50 % of the entire genome is covered by ≥ 30 nucleosome core reads in all the tissue types except for HNI testes (~16 reads)

From: Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species