Tom's innocence is apparent to readers because of logic. Mayella had a black eye on her right side of her face. This would indicate that a left-handed person struck her. In Chapter 17, Atticus shows the jury that Bob Ewell is left-handed. Yet in Chapter 18, Tom stands up and the courtroom notices, "His left arm was fully twelve inches shorter than his right, and hung dead at his side. It ended in a small shriveled hand, and from as far away as the balcony I (Scout) could see that it wad no use to him."
Atticus says the state has not produced any medical evidence that the crime that Tom was charged with ever took place.