1. A method of recovering a nucleic acid sequence using a probe map, the method comprising: aligning a probe having a base sequence of a predetermined length onto a target sequence based on a result in which the probe is hybridized to the target sequence; determining a representative value representing each aligned position of the probe based on a statistical distribution of each aligned position of the probe; and recovering a base sequence of the target sequence by using a probe map to which the determined representative values and base sequence information of the probe are mapped, wherein the aligning and determining steps are repeated for other probes having base sequences different from the probe, and the probe map contains mapping information of all aligned probes.