Chicago Mayor Rahm Emanuel’s administration is leaving a West Side police commander in his post despite an April recommendation by the city’s Independent Police Review Authority that his police powers be stripped.

The recommendation followed a DNA test bolstering a complaint that Harrison District Cmdr. Glenn Evans, 52, assaulted a South Side arrestee.

The complaint, according to sources close to the case, alleges that Evans threatened to kill Rickey J. Williams, 24, and jammed his police pistol into the man’s mouth. The sources spoke on condition they not be identified because they are not authorized to speak with the media.

The DNA test, described in an April 17 laboratory report from the Illinois State Police, found that material swabbed from the weapon “matches the DNA profile” of Williams.

IPRA, the city agency that investigates complaints of excessive police force, referred the case to Cook County State’s Attorney Anita Alvarez’s office for criminal investigation. An Alvarez spokesperson said the office is “not in a position at this time to make any public comment about the case.”

Read all our coverage about Cmdr. Glenn Evans

Spokespersons for police Supt. Garry McCarthy and Mayor Emanuel said they would not comment on the complaint because of the ongoing investigations.

The incident took place January 30, 2013, near the corner of East 71st Street and South Eberhart Avenue, according to a police report about the arrest. Evans, a commander who takes pride in patrolling the streets, was on duty in Grand Crossing, a South Side district he commanded at the time.

Evans spotted Williams with a blue-steel handgun in his pocket and chased the man on foot into an abandoned building, according to the arrest report. At least two other officers joined Evans on the scene.

Williams’ complaint, as described by the sources, alleges that a taser gun was pressed into his crotch while Evans held the police pistol in his mouth.

Reached by WBEZ, Evans declined to comment.

Vincent L. Jones, an IPRA investigator on the case, declined to comment or provide a copy of the complaint.

After the arrest, police and fire personnel searched the area but did not find the gun Williams allegedly possessed, according to another source close to the investigation.

Neither Evans nor the assisting officers filed a tactical response report as required when unusual force is used.

Williams was charged with misdemeanor reckless conduct. Months later, according to court records, officials dropped the charge when Williams demanded a trial.

Williams could not be reached for comment. Illinois is holding him in Pontiac Correctional Center, a downstate prison, for offenses unrelated to his encounter with Evans. Williams’ record includes felony convictions for possessing marijuana and violating electronic-monitoring terms.

As Williams began his prison sentence, IPRA’s investigation of Evans continued. Based on the lab results, the agency sent a memo to McCarthy, the police superintendent. The memo, signed by IPRA Chief Administrator Scott Ando, points to the DNA match and recommends that the police department relieve Evans of his police powers and “evaluate” the commander’s assignment.

Ando did not answer WBEZ questions about the case. His spokesman said IPRA could not comment because the investigation is ongoing.

Evans has been the subject of several lawsuits alleging excessive force or other misconduct. Those suits have led to at least two settlement payouts by the city.

Evans is also among 662 Chicago officers with more than 10 misconduct complaints during the five years that ended in May 2006, according to long-sought records the city released Tuesday. During that period, Evans had 14 complaints, none of which resulted in discipline.

Many rank-and-file officers and some community members have called Evans’ policing style appropriate for the tough districts in which he has served. McCarthy himself has praised Evans’ work repeatedly.

Chip Mitchell is WBEZ’s West Side bureau reporter. Follow him on Twitter @ChipMitchell1 and @WBEZoutloud, and connect with him through Facebook, Google+ and LinkedIn.