Sequence reads from representative region using Direct Capture and JumpStart Sequencing. Representative sequence reads from one region of BRCA1 exon 16 in the forward (black) and reverse (blue) directions are shown for the NA14096 sample. In the top half of the figure with Direct Capture Sequencing, horizontal black and blue arrows show where sequencing begins after each capture primer. In the lower half of the figure with JumpStart Sequencing, start sites were randomized by extension with polymerase prior to sequencing. A histogram for start sites is shown in Supplemental Figure S4. Sequence reads are aligned to the reference in the center (bold) and differences noted in red for substitutions, with dashes for deletions, and with bolded, underlined bases for insertions. Gaps are included between sequences so that individual reads can be distinguished. Random errors occur throughout the reads, but these are easily distinguished from real variants in which differences from the reference occur much more often (downward red arrow). This position corresponds to dbSNP variant rs1799966, a common substitution SNP. The reads shown are a sampling of those obtained for this region.