1. An image pickup device including a plurality of pixels arranged in two dimensions, one type of filter from among plural types of filters having different spectral characteristics being formed on each of the plurality of pixels, the image pickup device comprising: a first pixel region including a plurality of image pixels each configured to generate and output an image pixel signal, and a plurality of phase difference pixels each configured to generate and output a phase difference pixel signal; and a second pixel region including a plurality of image pixels each configured to generate and output an image pixel signal and including no pixel configured to output a valid phase difference pixel signal, wherein the plural types of filters are arranged on the plurality of image pixels in the first pixel region according to a predetermined arrangement pattern, for the plurality of phase difference pixels, a first type of filter from among the plural types of filters is formed on each of the phase difference pixels, and a part of the plurality of phase difference pixels is arranged at a regular position that is a position at which the first type of filter is formed where the predetermined arrangement pattern is applied to positions of the phase difference pixels and another part of the plurality of phase difference pixels is arranged at an irregular position that is a position at which a type of filter that is different from the first type of filter is formed, and a basic arrangement pattern of filters in the second pixel region is equal to a basic arrangement pattern of filters in the first pixel region.