The $3.98 represents "comprehensive income", a non-GAAP number that the company uses to show the economic value added as a result of their excellent management. It includes alot of items including the revaluation of the mortgage portfolio to current market prices. This number is not used to calculate the PE ratio.
The PE ratio is calculated using GAAP net income. (Share Price/Full Year's GAAP net income/share). The GAAP net income for AGNC's last 4 quarters was $3.02/share. Assuming a stock price of $33/share, the PE ratio would be 10.92. In the June quarter, AGNC posted a GAAP loss of $.88/share. This hurt their PE ratio badly.