Fig. S1. Effect of primer concentration on amplified copy number.

Fig. S2. Relative recovery proportions at various stages of 3D analysis.

Fig. S3. 3D analysis of mtDNA isolated from PolgWT and PolgD257A knock-in mice.

Fig. S4. Analysis of mitochondrial DNA copy number from human brain tissue samples.

Fig. S5. Analysis of ddPCR droplet counts from sequenced patient samples.

Fig. S6. Deletion sites are not fully saturated.

Fig. S7. Distribution of positive droplets from ddPCR of human brain.

Fig. S8. High resolution analysis of deletion dynamics.


Data S1. Supplementary notes, methods and figures.

Data S1A. Optimization of amplification factors.

Data S1B. Residual amplification bias.

Data S1C. Biases inherent in downstream applications.

Data S1D. Validation in biological samples.

Data S1E. Validation of sampling and analysis.

Data S1F. Disruption of droplet emulsions

Data S2. Tables of all accepted deletions for each patient. Sequence data deposited in the NCBI Sequence Read Archive under project accession number SRP027401.


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