AUSTIN — The Texas Department of Public Safety fired the state's top counterterrorism official Tuesday after he was arrested and accused of violently raping his wife’s friend.

John Jones, 45, who led the agency’s Intelligence and Counterterrorism Division, is charged with sexual assault and was being held in Travis County Jail Wednesday on bail of $750,000.

In a statement, the Department of Public Safety said the investigation is still active.

"The department takes allegations like this very seriously, and the Texas Rangers are working closely with the Travis County District Attorney's Office and the Travis County Sheriff's Office, which is leading this investigation," the department said.

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The alleged assault took place during a party at Jones’ house in Travis County on July 20. Jones had been drinking all day before he offered to take the woman on an ATV ride around 9 p.m., the arrest warrant said. With Jones seated behind her, the woman initially drove on streets before Jones suggested they go off-road. He then “aggressively” reached around her and took control of the vehicle, driving the pair into a brushy clearing where he pulled her off the ATV and raped her, the affidavit said.

Jones then drove them back to his house and told the woman not to tell anyone what happened, according to the sheriff’s report. Back at the party, however, the woman called to confide in a friend and then went to an emergency room with her mother, the report said. An exam found bruising and signs of trauma on her body, the report said.

Jones' attorney, Daniel Betts, said his client vehemently denies the allegations and "looks forward to combating them in court."

A former Navy SEAL, Jones has worked for the Department of Public Safety since 2009, during which time his department has won accolades for its work gathering, analyzing and sharing “threat-related information” with federal, state and local law enforcement. He was paid nearly $200,000 a year to oversee 150 analysts across Texas and provide timely information to prevent threats, including assisting the Texas Rangers, Border Security Operations and Texas Highway Patrol, according to his 2016 speaker biography by the Capital Area Council of Governments.

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In January, Jones met with President Trump at the White House for a roundtable discussion on border security and safe communities. During the meeting, Jones told Trump that over the past seven years there have been“over 4,000 people incarcerated that are illegal aliens in Texas jails for sexual assault.”

“The sad thing is, 62 percent of them are sexual assault against children. And those are Texas children. Those are American children. Those are our children,” he said. “And for anybody to put a price on any child’s life — that’s our most precious and cherished national treasure, and we should do everything and anything as public safety servants, as parents, and as leadership to protect those children.”

“And closing up that border to the bad people would be a great thing, John,” Trump said.

The woman cited Jones’ meeting with the president while describing him to the police as a “pillar of the community” who she knew was a well-respected, high-ranking law enforcement official and a military veteran. Before joining DPS, Jones was in the Navy for nearly 30 years, according to his LinkedIn page. During that time Jones was a Task Force Commander at SEAL Team Five, which conducted special operations in the Pacific and the Middle East.

The woman told a detective that on the day of the alleged assault, Jones was drunk by the afternoon and he passed out, then woke up later in the evening and began drinking again. At the party, she overheard Jones telling his daughter how to respond to a bully, by beating them “until the white shows” — meaning the bone, the affidavit said. The woman said the way Jones carried himself, with such bravado, she knew she would be no match for him if she resisted.