Starting around December 2019, an epidemic of pneumonia, which was named COVID-19 by World Health Organization (WHO), broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named SARS-CoV-2 by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses (ICTV) was soon found to be the cause. At present, the sensitivity of clinical nucleic acid detection is limited, and it is still unclear whether it is related to genetic variation. In this study, we retrieved 95 full-length genomic sequences of SARAS-CoV-2 strains from the NCBI and GISAID databases, established the reference sequence by conducting multiple sequence alignment and phylogenetic analyses, and analyzed sequence variations along the SARS-CoV-2 genome. The homology among all viral strains was generally high, among them 99.99% (99.91%-100%) at the nucleotide level, 99.99% (99.79%-100%) at the amino acid level. Although overall variation in ORF regions is low, 13 variation sites in 1a, 1b, S, 3a, M, 8, and N regions were identified, among which positions nt28144 in ORF 8 and nt8782 in ORF 1a showed mutation rate of 30.53% (29/95) and 29.47% (28/95) respectively. These findings suggested that there may be selective mutations in SARS-COV-2, and it is necessary to avoid certain regions when designing primers and probes. Establishment of the reference sequence for SARS-CoV-2 could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS-CoV-2 infection in the future. This article is protected by copyright. All rights reserved.