About a quarter of that crime had sexual overtones.
Over the last six years, 2005-06 through 2010-11, an analysis of incident data by The Inquirer uncovered 45 serious incidents at Germantown High in a basement area or stairwell. These crimes included assaults, morals offenses, robberies, and disorderly conduct that resulted in injury.
Eleven of them were sex offenses.
Basement or stairwell incidents represent 11 percent of the nearly 400 similar offenses that happened anywhere at the school.
About 40 percent of all sex offenses at Germantown - 11 of 27 - took place in stairways or a basement, the analysis showed. The incidents include forced and consensual acts as well as other morals offenses.
In each of the six previous years, there had been at least one morals offense in a basement stair area.
A problem with surveillance in Germantown's stairwells was highlighted by Safe Havens, a Georgia-based company hired by the state in 2010 to evaluate safety in some of Philadelphia's most dangerous schools.
Safe Havens also found problems with other unused areas of the high school in the review, deeming them "significant hazards."
The report included a picture of an unspecified "unlocked and unattended space" at Germantown that it said "poses a danger to students and staff because aggressors sometimes attack victims in these types of spaces."
Germantown is not the only school criticized by Safe Havens. The firm said unlocked classrooms, closets, auditoriums and boiler rooms frequently had been sites of sexual attacks elsewhere in the district. Two rapes were reported in district schools in unlocked rooms during school hours in the 2008-09 school year, Safe Havens said in the report.
Myron Patterson, the school district's chief safety executive, said monitoring all areas of the system's sprawling, aging school buildings posed a challenge.
"What you're dealing with is limited resources, antiquated buildings, structures from the early 1900s. From the security aspect, it makes it hard," he said. "It's unfortunate that that incident happened."
A security camera was operating in the school's basement, where the alleged attack occurred. Footage was turned over to police, Patterson said.
Some cameras are monitored by staff, and others record footage, he said.
Even with cameras and adults patrolling, it is impossible to prevent all crime, Patterson said.
Since the alleged rape, district officials have reviewed safety procedures with staff at Germantown to see how such incidents can be prevented, he said.
With tens of thousands of empty seats in the shrinking school district, vacant, little-used areas are becoming more prevalent.
Patterson said some schools had closed off unused sections of their buildings. The area of the Germantown High attack, however, was used by maintenance staff, he said.
The school walled off a wing from the 1950s that was not being used. The rest of the building at one time accommodated about 1,800 students and now has about 800.
"Clearly, these areas do present a safety challenge," said Kelley Hodge, the state-appointed safety advocate for Philadelphia schools.
"I'm sure if that particular area should have been secured and was not, that's an issue. If it was not on the list of places that should be secured, clearly it should be."
Hodge said she had spoken to the victim's mother. The family is relatively new to the Philadelphia area, she said.
"She's just trying to pay close attention to her daughter. She's a victim of trauma," Hodge said.
Hodge plans to introduce the family to counseling services, including Women Organized Against Rape, she said.
Hodge said she had been to Germantown High in recent weeks for a bullying and school safety seminar put on by the U.S. Attorney's Office. She spoke highly of principal Margaret Mullen-Bavwidinsi and the school.
"I was impressed with the proactive steps that Germantown High was taking," she said.
Mullen-Bavwidinsi could not be reached Thursday through a school district spokesman.
In last week's alleged rape, the boy was charged with multiple felony and misdemeanor offenses, including rape, unlawful restraint, false imprisonment, sexual assault, aggravated indecent assault, indecent exposure, simple assault, and reckless endangerment.
He apparently was new to the school, according to a source with knowledge of district records. The records showed that he enrolled at Germantown on April 30 and received his identification card May 3, a day before the alleged attack.
It could not be learned where he had attended school before Germantown.
School district spokesman Fernando Gallard would not comment on the student's education records.
The Inquirer was awarded the Pulitzer Prize for public service for its investigation of school violence. Read the series and find exclusive multimedia at www.philly.com/assault
Contact Dylan Purcell at 215-854-4915 or firstname.lastname@example.org, or follow on Twitter @dylancpurcell.