Many deletions that provide unique coverage of the Drosophila genome have been characterized only by polytene cytology and/or complementation analyses. Their breakpoints have not been mapped molecularly. Nevertheless, these deletions are important components of the Bloomington Deficiency Kit. In order for these deletions to be displayed on GBrowse along with molecularly defined deletions, it has been necessary to estimate the genomic coordinates of the breakpoints.
I examined the available data referenced by FlyBase aberration entries and from tests we have performed at the Bloomington Stock Center and generated estimates for the genomic positions of the breakpoints of 62 deletions and two related duplications. I made judgment calls when the data on any particular deletion was inconsistent. Investigators using these deletions or duplications experimentally should check that the estimates are valid and they should look for new data to refine the estimates.
The genomic coordinates of terminal deletions posed a problem for display. Terminal deletions are generated by a single breakpoint in a chromosome arm, but they delete segments that extend from these internal breakpoints to telomeres. For the purposes of displaying such deletions in GBrowse, the telomeres must be treated as a "breakpoints".
The proximal breakpoints of deletions that extend into centric heterochromatin have been shown as the proximal ends of current genome assemblies, even though the breakpoints lie closer to the centromeres. This was a convenience for the purpose of display on GBrowse.