What Causes Brown Vaginal Discharge After Having Intercourse?

i found out 6 weeks ago that i had chlamydia, myself and my partner were both treated. In the last few weeks i've been feeling pain in my back on the right side (level with my waist) and in my right thigh and down my right leg and also across the front of my ribs and at times in my upper back (it hasn't been an intense pain, more uncomfortable). i've also been feeling a little bit nauseous. i went to see my doctor last week who said that as i had no pain in my lower abdomen it was likely muscular and that taking ibuprofen should help. since then I've had some very dark brown/almost black mucus after having sex around the middle of my cycle - is this related in any way?