{
  "version": "2026.09.10",
  "common": {
    "collision_qc_bin_size": 10000,
    "microc_minimum_contacts": 200,
    "microc_short_inward_bp": 200,
    "microc_minimum_query_coverage": 0.8,
    "microc_long_range_cis_min_bp": 10000,
    "minimum_raw_reads": 500,
    "minimum_complete_units": 200
  },
  "profiles": {
    "ont_native": {
      "mapq": 20,
      "dedup_tolerance_bp": 0,
      "dedup_order": "after_contact_selection",
      "dedup_method": "exact unordered strand-aware aligned 5-prime endpoints within index scope"
    },
    "matched_comparison": {
      "mapq": 30,
      "dedup_tolerance_bp": 1,
      "dedup_order": "before_contact_selection",
      "dedup_method": "transitive strand-aware aligned 5-prime endpoints within index scope"
    }
  },
  "primary_chromosomes": {
    "dm6": [
      "chr2L",
      "chr2R",
      "chr3L",
      "chr3R",
      "chr4",
      "chrX"
    ],
    "hg38": [
      "chr1",
      "chr2",
      "chr3",
      "chr4",
      "chr5",
      "chr6",
      "chr7",
      "chr8",
      "chr9",
      "chr10",
      "chr11",
      "chr12",
      "chr13",
      "chr14",
      "chr15",
      "chr16",
      "chr17",
      "chr18",
      "chr19",
      "chr20",
      "chr21",
      "chr22",
      "chrX"
    ]
  },
  "definitions": {
    "cis_ratio": "cis contacts / all unique valid contacts",
    "long_range_cis_fraction": "cis contacts at or above configured distance / all unique valid contacts",
    "long_range_within_cis_fraction": "long-range cis contacts / all cis contacts",
    "collision_oe": "observed midpoint same-bin pairs / (N choose 2 * uniform-base null); terminal-bin widths corrected",
    "uncertainty": "Wilson 95% intervals assume independent contacts; molecule-subset 5th-95th percentile bands are conditional sampling ranges",
    "classification": "No default biological success/failure classification. Contact-count sufficiency is an evidence descriptor."
  }
}