Fig. 1

DNA shearing to 130 and 170 bp fractions before Illumina adapter ligation; sequencing base quality. a DNA insert length distribution per sample. b Peak insert lengths for the two different sample groups. c Alignment histograms for 130 bp insert samples (red) exhibited high amplitudes of coverage within the exon in comparison to 170 bp (blue) as exemplified by this gene BMP4 via IGV. Target regions of Agilent v5 and v5+UTR are given in the last two lines. Please note the 3 × fold higher maximum coverage of 130 bp samples. d High Phred score quality values for mapped paired-end reads. Base calling quality was high after trimming and mapping to the human genome. As expected, for both reads in forward and reverse direction (1–100 and 101–200 bases) read quality increased during the first 10 cycles and dropped gradually due to de-phasing errors of Illumina’s sequencing pipeline. After joining paired-end reads, quality scores improved between 75–125 cycles, as the best scores were kept while merging. Quality scores were ≥30 throughout nearly all cycles and similar between 130 and 170 bp samples