Figure 2

Non-uniform per-base sequence coverage. The 100-kb interval on chromosome 3 encoding the SCN5A gene (blue rectangles and joining lines) was amplified using eight LR-PCR amplicons (red filled rectangles in upper panel). On the y-axis, the fold sequence coverage scale is shown for each platform. The upper panel shows that amplicon end sequences are highly overrepresented. The y-axis was set to show the relative fold coverage of the sequences in the interval and therefore does not accurately represent the maximum fold coverage of the amplicon ends, which was 311, 195,473, and 15,041 for Roche 454, Illumina GA, and ABI SOLiD, respectively, in the sample shown. The lower panel shows the non-uniformity of sequence coverage across an approximately 17-kb region encompassing four exons of SCN5A. The locations of the repetitive elements (lower black/gray rectangles) in the interval are shown.