HIV DNA integration sites and genomic annotation mapped on the human genome. The human chromosomes are shown numbered. Unsequenced regions are shown in gray. The uppermost track on each chromosome indicates the locations of (1) ENCODE regions and (2) loci showing either greater or less HIV integration than predicted by the multiple regression model. ENCODE regions hosting more integration events than predicted (using a false discovery rate of 5%) are shown in red, those showing less are colored blue, and those ENCODE regions that contain sites not significantly different from that predicted by the model are colored black. Genome-wide loci showing greater integration than predicted are shown in red (hot) or orange (warm), indicating regions with 10 (red) or 50 (orange) sites where fewer were expected. Gray (cool) indicates regions with at least 10 integration events, where more were expected. Proceeding downward, integration site densities for the HIV-Mse (green; densities color-coded ranging from zero to 103 sites per 500-kb genomic segments) or HIV-Avr (red; ranging from one to 122 sites per 500-kb window) are shown in the next two (wider) tracks. In the next track down, the blue gradient indicates the number of Refseq transcription start sites, ranging from zero to 66 sites, located in a given 500-kb window. The next track (purple) shows Refseq gene coverage density, which quantifies the fraction of a given 500-kb window (0%–100%) that contains Refseq transcription units. The bottom track (brown) shows the G/C content (33%–61%) averaged over 500-kb intervals.
