Figure 4

Use of mapped partial reads to confirm calls and identify exact breakpoints. We tested for over-representation of tag start or end across predicted CNV breakpoint, and then mapped partial reads to identify exact breakpoints. We confirmed an 899 bp PTEN deletion present in two samples, a 510 bp deletion in BRCA1, and a 31 bp homozygous deletion in BRCA2 using this method. a) Unique breakpoint region for each CNV with sequence tags plotted by start and end position. Tags where all 76 bases align are shown in black, and tags where less than 76 bases align are shown in red. Z-scores generated based on the number of reads that start or end at each base are shown below the mapped reads with red indicating breakpoint(s). b) Each read that partially maps to the breakpoint aligns to sequence flanking the other side of the CNV, allowing exact breakpoint identification. Partial reads are shown in red, with a line connecting the two segments of each read. Length for all reads shown is 76 bp.