## 3 Results
Coverage is color coded using a _viridis_ colormap (reversed), with darker purple indicating higher coverage and yellow-green representing lower coverage. The coverage scale is based on the 85 th percentile. MT-RNR2 region is highlighted with a red line in the gene track and annotated with its specific coverage values. **(B)** Circular visualization of mitochondrial DNA coverage from whole genome sequencing (WGS) of the same MSC cell line. **(C–H)** IGV visualization of mitochondrial DNA sequencing data. Panel **(C)** shows the coordinate range of the mitochondrial genome. Panel **(D)** presents variant call files highlighting SNP and SV locations (blue lines). Panel **(E)** displays haplotype blocks of co-inherited variations. Panels **(F,G)** show aligned reads from AdMSC targeted and whole genome sequencing, respectively, with colored lines indicating variations. Panel **(H)** depicts OXPHOS-related genes with transcription directions (arrows). Comparative analysis revealed distinct coverage patterns between adaptive sampling (AS) and whole genome sequencing (WGS) approaches (Tables 1 and 2). AS yielded an average coverage of 157.5\(\times\) (112.8\(\times\) genome average enrichment), with notable over-enrichment in the MT-RNR2 region (694.4\(\times\), 497.4\(\times\) genome average) compared to other mitochondrial genes. This region exceeded the enrichment threshold of 135.6\(\times\) (2\(\times\) median enrichment). In contrast, WGS of the same MSC cell line demonstrated more uniform coverage (305.9\(\times\) average, 273.6\(\times\) genome average enrichment) across all mitochondrial genes, with no regions exceeding the over-enrichment threshold of 543.7\(\times\). The highest WGS coverage was observed in MT-ND2 (326.6\(\times\), 292.1\(\times\) genome average), while the lowest was in MT-ND6 (290.4\(\times\), 259.8\(\times\) genome average). The IGV visualization further revealed variant locations throughout the mitochondrial genome, with both SNPs and structural variations clearly identified. Haplotype blocks \begin{table}
\begin{tabular}{c c c} \hline \hline
**Metric** & **Adaptive Sampling** & **WGS** \\ \hline Average mtDNA Coverage (\(\times\)) & 157.48 & 305.95 \\ \hline Average Genome Coverage (\(\times\)) & 1.40 & 1.12 \\ \hline Overall Enrichment Factor & 112.81\(\times\) & 273.64\(\times\) \\ \hline Median Enrichment Factor & 67.80\(\times\) & 271.85\(\times\) \\ \hline Enrichment Threshold (highlight) & 135.60\(\times\) & 543.69\(\times\) \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Overall sequencing statistics. \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Gene/Region** & **Adaptive Sampling** & **Adaptive Sampling** & **WGS** & **WGS** \\
**Coverage (\(\times\))** & **Enrichment (\(\times\) Genome Avg)** & **Coverage (\(\times\))** & **Enrichment (\(\times\) Genome Avg)** \\ \hline MT-RNR2 & 694.4 *** & 497.4 *** & 295.0 & 263.8 \\ \hline MT-ND1 & 189.0 & 135.4 & 305.3 & 273.1 \\ \hline D-loop & 109.8 & 78.6 & 304.0 & 271.9 \\ \hline MT-ND5 & 106.3 & 76.2 & 303.9 & 271.8 \\ \hline MT-ND4L & 104.7 & 75.0 & 297.4 & 266.0 \\ \hline MT-CO3 & 97.8 & 70.1 & 297.3 & 265.9 \\ \hline MT-ATP6 & 95.6 & 68.5 & 308.8 & 276.2 \\ \hline MT-ND6 & 95.0 & 68.0 & 290.4 & 259.8 \\ \hline MT-ND4 & 94.3 & 67.6 & 304.2 & 272.1 \\ \hline MT-ATP8 & 90.0 & 64.4 & 311.3 & 278.4 \\ \hline MT-ND3 & 89.8 & 64.4 & 300.2 & 268.5 \\ \hline MT-CYB & 89.1 & 63.8 & 302.5 & 270.6 \\ \hline MT-CO1 & 85.5 & 61.3 & 317.2 & 283.7 \\ \hline MT-CO2 & 78.3 & 56.1 & 322.8 & 288.7 \\ \hline MT-ND2 & 75.5 & 54.1 & 326.6 & 292.1 \\ \hline MT-RNR1 & 74.0 & 53.0 & 292.4 & 261.5 \\ \hline \hline \end{tabular}
\end{table} 
Table 2: Nanopore sequencing coverage * and enrichment **. Adaptive sampling is compared to WGS. showing co-inherited variations were also visible, providing insight into the inheritance patterns of mitochondrial variants (Figure 5B).