SVs, CN, zygosity and allele frequency along chromosomes 3 and 11. Arcs in the top panels labeled “Events” represent the predicted connections between fragments derived from SV calls based on read pair orientation and spacing. Different read pair signatures indicate the following event types: deletions, tandem duplications, inversions, and interchromosomal translocations. The center panel (“Copy Number”) represents the CN estimates in 10-kb bins (gray) overlaid with their segmentation (black). The associated CN is shown on the y-axis. The zygosity track shows the proportion of homozygous SNV calls in 10-kb bins; darker purple regions contain more homozygous calls (up to 100%) and indicate potential LOH. The bottom panel shows the allele frequency distribution as a heatmap in 10-kb bins on the chromosome axis and 5% bins on the allele frequency axis; darker blue indicates more SNVs with the given allele frequency in the corresponding 10 kb region. The color scale is according to the log of proportion of SNVs falling into the allele frequency bin (e.g., 10–15%, i.e., the row) in the 10 kb region (i.e., the column). The chromosomal subregion 11q13, which is known to contain tumor-suppressor genes, is delineated with black bars.