Fig. 2: Graphical representations of copy number alterations (CNAs) and allelic fractions (AFs) from two tumors per patient.

Two tumors are obtained from each patient, represented on the left and right of the figure. Data from four patients with matched normal samples are available, and four sets of CNAs and AFs plots are presented. Within each set, the CNA plot is shown above the AF plot. For the CNA plot, the y-axis is the log2 ratio of the copy numbers of tumor to normal sample, both normalized for read depth. Points close to 0 (midline) represent no change in copy number, above 0 are copy gains, and below 0 are deletions. Regions are colored as follows: bright green (homozygous deletion), green (hemizygous deletion), blue (diploid heterozygous or copy-neutral loss of heterozygosity), dark red (copy number gain), and red (allele-specific CNA, unbalanced CNA, balanced CNA). The x-axis represents chromosomes. For the AF plot, the y-axis is the frequency of the reference allele in a germline heterozygous SNV, and the expected heterozygous frequency of 0.5 is the midline. Data points close to 1 represent homozygous reference, and data points close to 0 represent the homozygous nonreference base. Regions are colored as follows: gray (heterozygous, or balanced CNA), bright green (homozygous deletion), green (hemizygous deletion), blue (copy-neutral loss of heterozygosity), dark red (copy number gain), and red (allele-specific CNA, unbalanced CNA). The x-axis represents chromosomes.