Reproducibility package for "Mutation-context kernels exhibit a hierarchy of positional and chemistry invariants across eukaryotes

This record contains the complete reproducibility package for the manuscript “Mutation-context kernels exhibit a hierarchy of positional and chemistry invariants across eukaryotes”. The archive includes frozen and prospectively specified analysis plans, canonical derived inputs, deterministic outputs, checksum manifests, source-provenance documentation, and portable reproduction scripts for the statistical endpoints reported in the manuscript and Supporting Information. The package reproduces the principal results concerning Cartesian positional specificity across sequence-context scales, chemistry-identity transfer across evolutionary and genomic domains, low-dimensional representation boundaries, methylation-state Cartesian persistence, the K3 matched-mask localization test, the Plantae CHG localization test, and the direct de novo mutation power-feasibility analysis. Large upstream third-party raw archives are not redistributed. Their original published sources, provenance information, and cryptographic hashes are documented in the package. The statistical endpoints reported in the manuscript can be re-executed from the canonical derived objects included here. Primary portable entry points: python reproduce_main_endpoints.py python reproduce_biological_localization_and_dnm.py The manuscript and Supporting Information describe the scientific interpretation, inferential boundaries, frozen criteria, and limitations of these analyses.