The woman said she remembers Thomas kissing her on an air mattress at Cox's apartment. She said she has a fuzzy memory of what happened that night after she and a girlfriend met Cox and Thomas at a club and suspected she had been drugged.
Under questioning from Cox's attorney, the woman said if something had happened with Thomas, she wouldn't have considered it rape.
"It wouldn't have been fine but I wouldn't have seen it as rape if he admitted it," she said, referring to Thomas.
She said Thomas denied that anything had happened. Later, she found out she was pregnant and contacted authorities on Oct. 28, 2010. Investigators say DNA tests indicate Cox is the father.
Thomas and Vaughn also submitted DNA samples and were cleared
The Associated Press isn't identifying the woman because she's an alleged victim of a sexual crime.
Cox has pleaded not guilty to one count of sexual assault while the victim was physically helpless and one count of sexual assault while the victim was incapable of determining the nature of the conduct. He faces two years to life in prison if convicted.
A witness list of those who are expected to testify in Castle Rock, 30 miles south of Denver, remains sealed although Douglas County District Court Judge Paul King told potential jurors that Thomas and two other Broncos - linebacker Wesley Woodyard, and special teams specialist Cassius Vaughn - could be called.
Vaughn was Cox's roommate at the time who said he was asleep in the apartment that night.