This scripts in this repo were used to quantify constraint across the human mitochondrial genome, and to generate all data and figures presented in our manuscript.
required_files: input files for code.
build_model: code used to build the mitochondrial mutational model, and to curate of de novo mutations used to quantify mutability.
calculate_oe: code for assessment of mitochondrial constraint across functional variant classes and loci.
regional_constraint: code used to identify regional constraint.
local_constraint code used to identify local constraint and generate the mitochondrial local constraint (MLC) score.
other: code for other analyses presented in the manuscript.
figure_scripts: scripts used for generating figures, video and datasets.
See the README in each directory for more information on contents.
The code was run using Python v3.10, R v3.6.1, and ChimeraX v1.3.