To achieve consistency, we extracted the same depth data for both platforms based on the sample with the lowest depth, ensuring that each sample had the same sequencing depth across platforms. The minimum allele frequency (MAF) on both strands was set 2% during mutation calling. The majority of mtDNA mutations in fresh tissue samples were detectable on both platforms, although each platform generated a small number of platform-derived mutations. Therefore, a high consistency was observed in the observed base substitution patterns of mtDNA mutations. Additionally, the level of heterogeneity in these mutations was also highly comparable between the two platforms. In fresh tissue, FFPE tissue, and PBMC samples, the occurrence of platform-derived mutations was relatively low. However, both platforms detected a significant number of platform-derived mutations in plasma and urine samples