What are my chances?

Hi all,
I remember visiting this forum during my undergrad search and found it extremely helpful, so here I am again during my graduate school search. I’m just a bit lost/really don’t even know what, if any, schools I have a chance at getting into. I’m applying for either Molecular Bio or Immunology PhD programs.

Here are my stats:
Undergrad university - a quarter school + co-op program; will graduate with a BS in Biology (concentration in pathology) and a minor in Chemistry.
GPA: Will graduate with a 3.2
GRE: Taking them at the end of this month officially, but have been getting 160-163s for both V and Q consistently on all practice tests and feel confident I’ll maintain that.
Research: I’ve done two 6-month stints in a research position at a big pharma company (and a third 6-month stint at the same company in a process documentation-based position). Both research positions were working with influenza vaccines; I’ve got a pretty wide list of lab techniques I feel confident in using as a result of these positions, and I’ve also learned a lot about method development. I have an independent study research position lined up for my final two terms of classes, where I’ll be working with more molecular biology manipulating Dictyostelium. I also have another research position lined up working with either cancer cells, or looking at viruses in the CNS (I have the choice here and am a little lost as to which one I’m going to focus on). I have no publications, although I do have an invention disclosure memo for the work I’ve done at my second research co-op. My research in the fall will also most likely lead to a publication, although I don’t know if it’ll be in the appropriate time frame for applications.
LOR’s: Confident on the two LORs from my research co-ops, and plan to ask my overseeing prof for my independent study to write the third. (I have another academic LOR I could request, but feel as though having all three LORs from research-related connections is better, please correct me if I’m wrong)

I know my GPA isn’t great. I was in the wrong program for my interests, and changed my major. I struggled with some personal issues up until my junior year (an emotionally abusive relationship that lasted way longer than it ever should have, mental health issues that I got counselling for, an assault leaving permanent damage) which I feel confident I can explain in my SOP (as they have all contributed to why I want to continue my education). My freshman year GPA wasn’t bad, but sophomore + prejunior year it tanked to about a 2.87 and has been upward trending since (being .04 away from Dean’s list last fall, and last winter making deans list with a 3.9)

I’m looking at the following schools, but am considering adding another one or two
-University of Washington - Seattle (I’d apply to both the Immunology program and the MCB program)
-Boston University - (Again, I’d apply to both Immunology program and the MCB program; the immunology program is at BUMC)

I’m also considering UConn, a UC (I still have to do more research on these schools to see which I’d apply to), and want to apply for Penn’s molecular biology program to see what happens (and maybe Brown too on that note because the northeast is lovely.)

It’s worth noting that UW looks at the last 90 quarter credits in terms of my GPA, so my GPA will sit more towards a 3.4. I’m not sure if this is a common practice or if there are other schools I could look at so my GPA is a bit more competitive.

Are there other schools I’m a better fit for that I’m missing out on? I feel like there are just so many schools and options, and because grad schools aren’t as numbers based as undergrads, I don’t really know what schools align with my stats. Do I stand a chance at all, or should I really be looking into masters programs?

I don’t think your GPA will keep you out of top programs, especially with the extenuating circumstances. However, don’t soley focus your SOPs on a GPA apology, be sure to cover all the bases.