An aspect of the present invention includes performing electrophoresis of a nucleic acid sample to be analyzed labeled for each base type, generating waveform data of detected intensity by detecting a label signal for the each base type, selecting another peak position for each peak position of the waveform data for each base type, calculating relative signal intensity of signal intensity in each position relative to the signal intensity in the other selected position, and analyzing existence of each base type in a base sequence coordinate position of the nucleic acid sample by comparing the relative signal intensity of the nucleic acid sample to be analyzed and the relative signal intensity of a known nucleic acid sample in each peak position. Accordingly, acquiring information about a gene mutation in trace amounts existing in a target gene region highly sensitively with high precision is realized.
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