A genetic characteristic estimation device (2000) acquires genetic mutation information (30) and position information (40). The genetic mutation information (30) indicates information regarding a genetic mutation in a deoxyribonucleic acid (DNA) sequence of a target cell (20) obtained from a target organism (10). In the position information (40), a position on the DNA sequence is associated with the type of a cell or the type of an organ. The genetic characteristic estimation device (2000) determines a genetic mutation at the position associated with the type of the target cell (20) or the type of an organ including the target cell (20) in the position information (40) from among genetic mutations indicated by the genetic mutation information (30), and computes a genetic characteristic index value representing a genetic characteristic of the target organism (10) based on a characteristic of the determined genetic mutation.