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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

  Collected reads Uniquely mapped reads Ratio of uniquely mapped reads Genome coverage
Hd-rR blastulae 339,407,788 220,270,276 64.90 % 46.3
Hd-rR testes 389,257,067 245,192,521 62.99 % 51.5
Hd-rR liver 342,386,421 233,904,210 68.32 % 49.1
HNI blastulae 391,519,667 291,165,889 74.37 % 61.1
HNI testes 587,561,947 336,898,284 57.34 % 70.7
HNI liver 467,963,072 343,765,549 73.46 % 72.2
Total 2,518,095,962 1,671,196,729 66.37 % 351.0
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