How Do UC's and Stanford Calculate GPA?

I know UC’s do not care about your freshman year, but my school says they calculate weighted and my total right now for sophomore year is 3.46.
Here are my grades
Anat/Phys B-/B-
Algebra 2 C-/A
Chinese 2 A-/A-
PE A/A-
Chemistry A/A-
English A/A-

I thought that my GPA would be higher, like 3.66, not 3.46. So I was wondering, how does it all go?

UC GPA calculator:
http://rogerhub.com/gpa-calculator-uc/
I get 3.6 with no.Honors or AP/IB classes. PE not counted. You really need to wait until end of Junior year to get an accurate GPA. Are you planning to take any Honors/AP classes since these schools will look at course rigor?