(a) Mapping of 7 captured libraries, including 2 biological replicates for two different treatments of mouse embryonic fibroblast cell lines (MEF): MEFmmS1 and MEFmmS2, MEFpmS1 and MEFpmS2, and one pair of technical replicates for mouse embryonic stem cell lines MESrep1 and MESrep2, and a negative control library without biotinylated probes (MESnobait). Mapping data is shown for each library, in which red color shows number of mapped reads, while blue colors shows unmaped reads, and yellow color shows reads mapped to ribosomal RNA genes, and purple shows low quality reads (i.e. reads with ambiguous N bases). The mapping data show that the capture protocol could remove most of ribosomal RNAs and most sequencing reads are mappable to the reference genome. (b) The base composition of each sequencing round (total 75 rounds for the first read, as shown by the horizontal axis from 1 to 75). Sequencing was performed using a MiSeq 150-cycle kit. Colour represents four A, C, G, and T nucleotides (in sequential order from bottom to the top) and an ambiguous class for N nucleotides (black colour). The vertical axis shows counts for each nucleotide type from each of the 75 sequencing rounds. In every sequencing round, all four nucleotide classes were detected.