Graphical view of proportion of strains displaying CNV for each sequence feature on each chromosome. A sequence feature is defined as either an annotated gene or the un-translated region (UTR) between two genes. CNV criteria were as follows: minimum log2 ratio of signal intensities (test strain/reference) +/- 0.6, minimum number of probes 5, tolerance for extending a CNV 0.1. At the top of each panel is a line drawing representing a chromosome. Vertical bars represent CNV that met the criteria for significance. Vertical bars above the line are amplifications and those below the line are deletions relative to CL-Brener. The height (depth) of the vertical bars is proportional to the number of strains showing that CNV. The vertical bars are colored to indicate strain type (type 1 and type 2) as follows: green, type 1 strains amplification; blue, type 1 strains deletion; maroon, type 2 strains amplification; yellow, type 2 strains deletion. Below each chromosome line drawing is a diagram representing the annotated chromosome. Genes are color coded based on annotation; named genes not belonging to large gene families (dark blue), hypothetical genes (light blue), trans-sialidases (red), mucin associated surface proteins (MASP) (burnt orange), mucins (orange), retrotransposon hotspot (RHS) proteins (green), dispersed gene family 1 (DGF) (gray), surface protease gp63 (purple).