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The coroner, Dr, John Penistan stated in his autopsy report that there were some bruising around Harper's vagina. In his report there are references to "contusions" and "abrasion". See the report.
See the full final autopsy report (.pdf file)
We asked Dr. John Butt, the former
chief medical examiner of Nova Scotia, about this
contradiction. Here is an excerpt from our interview:

MACINTYRE: No bruise.
BUTT: No bruise. So there are 2 points here. One is, that was never reported. But at the same time the absence of a bruise was subsequently used to make a conclusion which was that the tissue wouldn'tbruise after death therefore the rape occurred after death. That really is a travesty because there was no opportunity for the defense to make a criticism over that area in the potential for the rape but a leap was taken to say yes there was a rape but it was post mortem.
MACINTYRE: After she died.
BUTT: Yes it was after she died. Now that's bad. And in fact it's, it's unprofessional. It's like me uh turning around and saying well I marked this down and it wasn't a knife wound but I'm leaving it there.See but I found out afterwards it wasn't a knife wound but a I'm leaving it in. I think that there that there's a travesty here and I would go so far as to say that if this correct and I believe it is correct, that this is this is unprofessional conduct.
The autopsy report does make mention of "contusions" and "abrasions in the genital area - bruising that most commonly is caused by sexual intercourse. There was no sperm found, but in court they cited a swollen vagina, a thick whitish fluid and marks all over body. But Dr. Ferris suggests " you can make a very good case that there may not have been rape at all." Harper was sexually assaulted, but Ferris argues there is not enough medical evidence to conclusively point to sexual intercourse.
Here is an excerpt of his interview with the fifth estate:

MACINTYRE: Let me read a couple of phrases from scientific laboratory evidence. Acid Phosphotase as it was found supposedly in great quantities in her body is "a constituent of semen, which comes from men and not naturally found in females."
FERRIS: That's wrong. That is simply wrong. Acid phosphotase is normally found in women.
MACINTYRE: They saw here that it is strong presumptive evidence of the presence of semen in the vagina.
FERRIS: That's simply wrong.
MACINTYRE: There's
a lot of talk about whitish fluid in very large
quantities as being evidence of a lot of sexual
activity. Now, how do you discount that?
FERRIS: This
is a body that is undergoing decomposition that
has been invaded by maggots that is in fact showing
a variety of decompositional changes. And whitish
fluid would be quite a normal finding in the vagina.
The fifth estate uncovered evidence
that backs him up. On Saturday, June 13, just hours
after that examination there was another. Dr John
Taylor, the jailhouse doctor examined him and concluded
that "with special reference
to his penis, ... he had not observed any injury."
Taylor's report never surfaced at his trial.
Here is a copy of that jailhouse report.