The SAM view of data under gbrowse does not display reads with large deletions correctly. When viewing at base level bgcolor (green) and '-' are seen. Next stage out a thin green line and zoomed out further they become completely undetectable.
I've attached a zip file with an image including the 3 levels of view, along with a BAM file containing the data used to generate the images. Data is mapped against Human GRCh37 (hg19).