1. A pattern inspection apparatus which inspects a pattern formed on a plate, comprising: a pattern data generator configured to generate measured pattern data regarding the pattern on the plate; a memory which stores first designed data and second designed data, the first designed data representing an opaque pattern including a first alignment mark and the second designed data representing a phase shifting pattern including a second alignment mark; a bit pattern data generator configured to provide first bit pattern data obtained by converting the first designed data to a two-dimensional image pattern data configured of squares in units of bit, and second bit pattern data obtained by converting the second designed data to another two-dimensional image pattern data configured of squares in units of bit; a positional corrector configured to correct a relative position between the phase shifting pattern and the opaque pattern by correcting data of the phase shifting pattern with respect to data of the opaque pattern by a difference between a measured data difference and a designed data difference to obtain first corrected bit pattern data and second corrected bit pattern data, the measured data difference concerning a difference of respective measured data of the first alignment mark and the second alignment mark which are obtained based on the measured pattern data, and the designed data difference concerning a difference of respective designed data of the first alignment mark and the second alignment mark; a reference pattern data generator configured to generate reference pattern data by combining the first corrected bit pattern data and the second corrected bit pattern data; and a comparator configured to compare the reference pattern data with the measured pattern data to inspect a defect of the pattern on the plate.