-methyladenosine (mA) is one of the most abundant messenger RNA modifications in eukaryotes involved in various pivotal processes of RNA metabolism. The most popular high-throughput mA identification method depends on the anti-mA antibody but suffers from poor reproducibility and limited resolution. Exact location information is of great value for understanding the dynamics, machinery, and functions of mA. Here, we developed a precise and high-throughput antibody-independent mA identification method based on the mA-sensitive RNA endoribonuclease recognizing ACA motif (mA-sensitive RNA-Endoribonuclease-Facilitated sequencing or mA-REF-seq). Whole-transcriptomic, single-base mA maps generated by mA-REF-seq quantitatively displayed an explicit distribution pattern with enrichment near stop codons. We used independent methods to validate methylation status and abundance of individual mA sites, confirming the high reliability and accuracy of mA-REF-seq. We applied this method on five tissues from human, mouse, and rat, showing that mA sites are conserved with single-nucleotide specificity and tend to cluster among species.