{
  "sample": "HL120",
  "method": "full_adapter_bounded_insert_BWA_MEM2_split_alignment",
  "status": "EXPLORATORY",
  "unit_of_analysis": "adapter_bounded_non_dimer_library_unit",
  "ligation_screened_units": 4749,
  "ligation_resolved_units": 3364,
  "ligation_unresolved_units": 1385,
  "ligation_resolved_fraction": 0.7083596546641399,
  "ligation_two_units": 2300,
  "ligation_three_units": 52,
  "ligation_four_units": 4,
  "ligation_five_plus_units": 0,
  "ligation_single_block_units": 1008,
  "ligation_multifragment_fraction": 0.4961044430406401,
  "ligation_multifragment_fraction_resolved": 0.7003567181926278,
  "category_counts": {
    "1": 1008,
    "2": 2300,
    "3": 52,
    "4": 4,
    "5+": 0,
    "unresolved": 1385
  },
  "raw_molecules_with_units": 4533,
  "scopes": {
    "lib01": {
      "ligation_screened_units": 4678,
      "ligation_resolved_units": 3308,
      "ligation_unresolved_units": 1370,
      "ligation_resolved_fraction": 0.7071398033347585,
      "ligation_two_units": 2259,
      "ligation_three_units": 52,
      "ligation_four_units": 4,
      "ligation_five_plus_units": 0,
      "ligation_single_block_units": 993,
      "ligation_multifragment_fraction": 0.49486960239418554,
      "ligation_multifragment_fraction_resolved": 0.6998186215235792,
      "category_counts": {
        "1": 993,
        "2": 2259,
        "3": 52,
        "4": 4,
        "5+": 0,
        "unresolved": 1370
      },
      "raw_molecules_with_units": 4476
    },
    "unassigned": {
      "ligation_screened_units": 71,
      "ligation_resolved_units": 56,
      "ligation_unresolved_units": 15,
      "ligation_resolved_fraction": 0.7887323943661971,
      "ligation_two_units": 41,
      "ligation_three_units": 0,
      "ligation_four_units": 0,
      "ligation_five_plus_units": 0,
      "ligation_single_block_units": 15,
      "ligation_multifragment_fraction": 0.5774647887323944,
      "ligation_multifragment_fraction_resolved": 0.7321428571428571,
      "category_counts": {
        "1": 15,
        "2": 41,
        "3": 0,
        "4": 0,
        "5+": 0,
        "unresolved": 15
      },
      "raw_molecules_with_units": 70
    }
  },
  "parameters": {
    "minimum_segment_bp": 40,
    "mapq": 20,
    "minimum_identity": 0.85,
    "minimum_query_coverage": 0.8,
    "maximum_query_gap": 30
  },
  "units_tsv": "/path/to/HL120.units.tsv.gz",
  "segments_tsv": "/path/to/HL120.segments.tsv.gz",
  "limitations": [
    "Resolved blocks are evidence-supported minimum fragment counts, not exact biochemical insert counts.",
    "Collinear or immediately adjacent genomic fragments may be indistinguishable from one continuous block.",
    "Short, repetitive, low-quality or unaligned internal fragments may be missed.",
    "ONT adapter-linked library units are not counted as Micro-C junctions; units sharing a raw molecule are dependent.",
    "No positive wet-lab ligation standards or no-ligation control have been supplied."
  ]
}