{
  "config": {
    "metric_profile": "ont_native",
    "output_dir": ".work",
    "default_reference": "dm6",
    "references": {
      "dm6": {
        "assembly": "dm6",
        "primary_chromosomes": [
          "chr2L",
          "chr2R",
          "chr3L",
          "chr3R",
          "chr4",
          "chrX"
        ],
        "fasta": "/path/to/dm6.fa",
        "chrom_sizes": "/path/to/dm6.chrom.sizes",
        "annotation": "/path/to/dm6.ncbiRefSeq.gtf",
        "bowtie2_index": "/path/to/dm6",
        "bwa_mem2_index": "/path/to/dm6.fa",
        "mycoplasma_index": "/path/to/index"
      },
      "hg38": {
        "assembly": "hg38",
        "primary_chromosomes": [
          "chr1",
          "chr2",
          "chr3",
          "chr4",
          "chr5",
          "chr6",
          "chr7",
          "chr8",
          "chr9",
          "chr10",
          "chr11",
          "chr12",
          "chr13",
          "chr14",
          "chr15",
          "chr16",
          "chr17",
          "chr18",
          "chr19",
          "chr20",
          "chr21",
          "chr22",
          "chrX"
        ],
        "fasta": "/path/to/hg38.fa",
        "chrom_sizes": "/path/to/hg38.chrom.sizes",
        "annotation": "/path/to/hg38.ncbiRefSeq.gtf",
        "bowtie2_index": "/path/to/hg38",
        "bwa_mem2_index": "/path/to/hg38.fa",
        "mycoplasma_index": "/path/to/index"
      }
    },
    "mycoplasma_screen": {
      "enabled": true,
      "target_contig_regex": "mycoplasma_target|mycoplasmopsis|mycoplasmoides|metamycoplasma|mesomycoplasma|acholeplasma|spiroplasma|ureaplasma|mollicutes",
      "minimum_screened_reads": 500
    },
    "spike_in": {
      "enabled": true,
      "mode": "auto",
      "database_manifest": "resources/spikein_v1/manifest.json",
      "declared_spike_in": false,
      "threads": 4,
      "minimum_aligned_bp": 80,
      "minimum_query_coverage": 0.8,
      "minimum_identity": 0.85
    },
    "alignment": {
      "chromatin_mapper": "bowtie2",
      "microc_mapper": "bwa-mem2"
    },
    "params": {
      "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,
      "mapq": 20,
      "dedup_tolerance_bp": 0,
      "dedup_order": "after_contact_selection",
      "dedup_method": "exact unordered strand-aware aligned 5-prime endpoints within index scope",
      "metric_profile": "ont_native",
      "metric_definition_version": "2026.09.10",
      "ligation_minimum_segment_bp": 40,
      "ligation_minimum_query_coverage": 0.8,
      "ligation_maximum_query_gap": 30,
      "annotation_promoter_window_bp": 2000,
      "gene_profile_upstream_bp": 5000,
      "gene_profile_downstream_bp": 5000,
      "gene_profile_body_bp": 5000,
      "gene_profile_bin_size": 100,
      "gene_profile_sublibrary_threads": 16,
      "karyotype_bins_per_longest_chromosome": 250,
      "karyotype_gene_window_bp": 250000,
      "size_trace_max_bp": 2000,
      "size_trace_bandwidth": 0.045,
      "single_index_pair_fraction": 0.9,
      "index_variant_max_edit": 2,
      "index_variant_dominance_ratio": 5.0
    },
    "qc_reference_ranges": {
      "raw_reads": {
        "min": 500,
        "warning_min": 250
      },
      "mean_read_q": null,
      "complete_read_rate": {
        "min": 0.5,
        "max": 1.0,
        "warning_min": 0.3,
        "type": "percent"
      },
      "adapter_dimer_rate": {
        "min": 0.0,
        "max": 0.05,
        "warning_max": 0.1,
        "type": "percent"
      },
      "primary_mapping_rate": {
        "min": 0.5,
        "max": 1.0,
        "warning_min": 0.3,
        "type": "percent"
      },
      "usable_fragment_rate": {
        "min": 0.3,
        "max": 1.0,
        "warning_min": 0.15,
        "type": "percent"
      },
      "mitochondrial_fraction": {
        "min": 0.0,
        "max": 0.2,
        "warning_max": 0.4,
        "type": "percent"
      },
      "both_legs_mapping_rate": {
        "min": 0.5,
        "max": 1.0,
        "warning_min": 0.3,
        "type": "percent"
      },
      "cis_ratio": null
    },
    "samples": {
      "HL240": {
        "fastq": [
          "inputs/8KXMVK_4_CR_HL240.fastq"
        ],
        "type": "chromatin",
        "reference": "hg38"
      },
      "HL120": {
        "fastq": [
          "inputs/TVKRTF_11_MC_A_HL120.fastq"
        ],
        "type": "microc"
      }
    },
    "tools": {
      "python": "python3",
      "bowtie2": "bowtie2",
      "bwa_mem2": "bwa-mem2",
      "samtools": "samtools",
      "bamCoverage": "bamCoverage",
      "computeMatrix": "computeMatrix",
      "plotProfile": "plotProfile",
      "bedGraphToBigWig": "bedGraphToBigWig",
      "rscript": "Rscript"
    },
    "report_dir": "report"
  },
  "created_utc": "2026-09-10T17:52:51.934957+00:00",
  "library_size_profiles": {
    "bandwidth": 0.045,
    "coordinate": "log1p(bp/50)",
    "count_based_default_collapsed": true,
    "length_definition": "insert + sequence-derived adapters and physical index lengths",
    "main_weighting": "length",
    "maximum_bp": 2000.0,
    "measured_fluorescence": false
  },
  "metric_definitions": {
    "matched_comparison": {
      "collision_qc_bin_size": 10000,
      "dedup_method": "transitive strand-aware aligned 5-prime endpoints within index scope",
      "dedup_order": "before_contact_selection",
      "dedup_tolerance_bp": 1,
      "mapq": 30,
      "metric_definition_version": "2026.09.10",
      "metric_profile": "matched_comparison",
      "microc_long_range_cis_min_bp": 10000,
      "microc_minimum_contacts": 200,
      "microc_minimum_query_coverage": 0.8,
      "microc_short_inward_bp": 200,
      "minimum_complete_units": 200,
      "minimum_raw_reads": 500
    },
    "native": {
      "collision_qc_bin_size": 10000,
      "dedup_method": "exact unordered strand-aware aligned 5-prime endpoints within index scope",
      "dedup_order": "after_contact_selection",
      "dedup_tolerance_bp": 0,
      "mapq": 20,
      "metric_definition_version": "2026.09.10",
      "metric_profile": "ont_native",
      "microc_long_range_cis_min_bp": 10000,
      "microc_minimum_contacts": 200,
      "microc_minimum_query_coverage": 0.8,
      "microc_short_inward_bp": 200,
      "minimum_complete_units": 200,
      "minimum_raw_reads": 500
    }
  },
  "metric_schema_version": 3,
  "python_version": "3.10.19 | packaged by conda-forge | (main, Oct 22 2025, 22:29:10) [GCC 14.3.0]",
  "example_selection": {
    "samples": [
      "HL240",
      "HL120"
    ],
    "synthetic": false,
    "source": "Existing ONT QC reports; numerical measurements and displayed sample figures are retained.",
    "paths": "Execution paths in metadata are portable placeholders. Raw inputs and reference indexes are not included."
  }
}