Relatives said Bettie Jones lived downstairs from Quintonio LeGrier, the 19-year-old subject of the initial call to police, who also was killed by the officer.
Officers who responded to the call "were confronted by a combative subject resulting in the discharging of the officer's weapon," the Chicago Police Department said in a brief statement.
"The 55-year-old female victim was accidentally struck and tragically killed," reads the statement, which extends "deepest condolences to the victim's family and friends."
The shooting happened around 4:25 am, police said. The Cook County medical examiner's office and family members said LeGrier, a 19-year-old college student, was pronounced dead at a hospital at 4:51 a.m. and Jones, a 55-year-old mother of five, died at a different hospital a short time later.
Both LeGrier and Jones were black, the medical examiner's office said. Police did not immediately disclose the race of the officer, nor how long the officer has been with the department or the officer's current work status.
The shooting comes amid a federal civil rights investigation of the Chicago Police Department launched after last month's release of police dashcam video showing white officer Jason Van Dyke shooting black 17-year-old Laquan McDonald 16 times in 2014. Officials have said the federal investigation will look into patterns of racial disparity in the use of force, as well as review how the department disciplines officers and handles misconduct accusations.
LeGrier's father told the Chicago Sun-Times he had invited his son to a family holiday gathering before the shooting but the younger man chose not to go. Antonio LeGrier said when he returned to his second-floor apartment early Saturday, his son appeared to be a "little agitated."
The elder LeGrier said he heard loud banging on his locked bedroom door around 4:15 a.m. and that his son said, "You're not going to scare me." He said his son tried to bust the door open, but he kept him from doing so and called police.
The father said he called Jones, who lived a floor below, and warned her that his son was a "little irate" and not to open the door unless police arrived. He said Jones told him she saw his son outside with a baseball bat.
When police arrived, Antonio LeGrier said he heard Jones yell, "Whoa, Whoa Whoa!" He said he heard gunshots as he made his way down from the second floor and then saw his son and Jones lying in the foyer.
"I identified myself as the father and I held my hands out," he said.
Jones' daughter, Latisha Jones, told the Sun-Times and Chicago Tribune that she woke up when she heard gunshots. She said she walked to the front door and saw her mother bleeding on the ground.
Antonio LeGrier said police later told him that Quintonio LeGrier was shot seven times, and that he had called police before his father did.
Chicago police on Saturday afternoon referred Associated Press requests for additional comment to the Independent Police Review Authority, the city's main police oversight agency. IPRA spokesman Larry Merritt said the agency was investigating an officer-involved shooting but said it was "very early on in the investigation" and he couldn't release further details. Autopsies, which would determine how many times LeGrier and Jones were shot, were not scheduled Saturday, medical examiner's office spokeswoman Becky Schlikerman said.
It is not clear from the initial police statement whether there are any video recordings of the shooting.
Antonio LeGrier told the Sun-Times that his son had emotional problems after spending most of his childhood in foster care. "Did it warrant him getting shot and killed? I don't believe it," the elder LeGrier said.
LeGrier described his son as a "whiz kid" and said he was home on holiday break from Northern Illinois University, where he majored in electrical engineering technology.
LeGrier's mother, Janet Cooksey, told the Chicago Tribune that despite her son's issues, police didn't have to react the way they did.
"We're thinking the police are going to service us, take him to the hospital. They took his life," said Cooksey, who was not present at the time of the shooting.
The release of the McDonald shooting video has led to protests, the forced resignation of former Chicago Police Superintendent Garry McCarthy and calls from residents for Mayor Rahm Emanuel to step down.
Cooksey said she wants a personal apology from Emanuel for what happened to her only child.
"Are we gonna get protected or is the police just gonna keep taking lives?" Cooksey said. "I mean, who's gonna answer these questions?"
Emanuel's office didn't immediately respond to a request for comment from the AP.
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