├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── __init__.py ├── gnomad_mitochondria ├── __init__.py ├── manuscript_analyses │ ├── README.md │ ├── __init__.py │ ├── annotated_synthetic.vcf.gz │ ├── chrM.pos2annot.txt │ ├── count_mnv.pl │ ├── figure_scripts │ │ ├── collate_figure5.R │ │ ├── generate_all_figs5_6_S5D_S7_S8_tables_S3_S4.R │ │ ├── generate_fig1.R │ │ ├── generate_fig1A_4_3BCD_S5ABC_S6.R │ │ ├── generate_fig2.R │ │ ├── generate_fig3E.R │ │ ├── generate_fig5A.R │ │ ├── generate_fig5B.R │ │ ├── generate_fig5C.R │ │ ├── generate_fig5DEF.R │ │ ├── generate_fig6.R │ │ ├── generate_figS2.R │ │ ├── generate_figS3.R │ │ ├── generate_figS4.R │ │ ├── generate_figS5D.R │ │ ├── generate_figS5EFG.R │ │ ├── generate_figS7.R │ │ ├── generate_figS8.R │ │ ├── generate_tableS3.R │ │ └── generate_tableS4.R │ ├── final_data_files │ │ ├── gnomad │ │ │ └── gnomad.genomes.v3.1.sites.chrM.reduced_annotations.tsv │ │ ├── insilicos │ │ │ ├── MitImpact_db_3.0.6.txt │ │ │ ├── get_hmtvar.py │ │ │ └── hmtvar_annotations.txt.zip │ │ ├── other_databases │ │ │ ├── HelixMTdb_20200327.tsv │ │ │ ├── MITOMAP_disease_02012021.cgi │ │ │ ├── MITOMAP_polymorphisms_02022021.cgi │ │ │ └── readme.txt │ │ └── synthetic_vcf │ │ │ ├── NC_012920.1.fasta │ │ │ ├── NC_012920.1_synthetic_vep.vcf.gz │ │ │ ├── NC_012920.1_synthetic_vep_splitvarstwogenes.vcf.gz │ │ │ ├── check_synthetic_vcf.py │ │ │ ├── make_syntheticvcf_mtDNA.sh │ │ │ ├── readme.txt │ │ │ └── split_vars_two_genes.py │ ├── merge_sets.pl │ ├── numtAB.txt │ ├── preprocess.step1.sh │ ├── preprocess.step2.sh │ ├── qc_plots │ │ ├── duplicate_qc_plots.R │ │ ├── mixins_plots.R │ │ └── na12878_plots.R │ ├── reformat_vcf.py │ └── vcf_to_table.nosplit.pl ├── mutserve_batch │ ├── Dockerfile │ ├── bashrc │ ├── mutserv_batch.py │ ├── process_mutserv.py │ └── rCRS.fasta ├── pipeline │ ├── __init__.py │ ├── add_annotations.py │ ├── annotate_coverage.py │ ├── annotation_descriptions.py │ ├── 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