After get the raw data of C4_mtscATAC, the first step was used for the C4_mtATAC data standard analysis to obtain cell clustering results for each sample. In the second step, merging all the clustering results of each samples is conducted and followed by cell type annotation using multiple tools. Step 3 for quantifying mitochondrial content and generating certain plots for different cell types. Step 4 involves SNP calling and filtering for each cell. All commands for each step were documented in the ReadME.txt file in corresponding directory.