Data deduplication is a technology that eliminates redundant data to save storage space. Most previous studies on data deduplication target backup storage, where the deduplication ratio and throughput are important. However, data deduplication on primary storage has recently been receiving attention; in this case, I/O latency should be considered equally with the deduplication ratio. Unfortunately, data deduplication causes high sequential-read-latency problems. When a file is created, the file system allocates physically contiguous blocks to support low sequential-read latency. However, the data deduplication process rearranges the block mapping information to eliminate duplicate blocks. Because of this rearrangement, the physical sequentiality of blocks in a file is broken. This makes a sequential-read request slower because it operates like a random-read operation. In this paper, we propose a selective data deduplication scheme for primary storage systems. A selective scheme can achieve a high deduplication ratio and a low I/O latency by applying different data-chunking methods to the files, according to their file access characteristics. In the proposed system, file accesses are characterized by recent access time and the access frequency of each file. No chunking is applied to update-intensive files since they are meaningless in terms of data deduplication. For sequential-read-intensive files, we apply big chunking to preserve their sequentiality on the media. For random-read-intensive files, small chunking is used to increase the deduplication ratio. Experimental evaluation showed that the proposed method achieves a maximum of 86% of an ideal deduplication ratio and 97% of the sequential-read performance of a native file system.