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  "alignment_realism": {
    "aggregate": {
      "background_population_record_classes": {
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          "fraction": 0.999073
        },
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        "supplementary": {
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        "unmapped": {
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          "fraction": 0.000927
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          "fraction": 1.0
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        },
        "RG_presence": {
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          "fraction": 1.0
        },
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        "clipped_bases": {
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          "median": 151.0,
          "min": 36.0,
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      "planted_record_classes": {
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    },
    "interpretation": [
      "Core alignment fields were computed by BWA-MEM, not copied or invented: AS, NM, MD, MAPQ, CIGAR, pairing flags, and conditional XS/SA co-vary with each alignment.",
      "The planted reads are intentionally chimeric. Higher clipping, discordant pairing, alternate alignments, or SA/secondary evidence than ordinary background is expected and is evidence of fusion structure, not proof that the reads are identical to natural molecules.",
      "The background match controls control identity, read end, and approximate read length, but not molecular library history or breakpoint locus. Original instrument FASTQs and original Picard/GATK intermediates were unavailable."
    ],
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          "target_window_ambiguous": false,
          "tier": "REVIEW",
          "total_support": 67
        },
        "fusion": "CD74-ROS1",
        "truth_identity_verified": true,
        "truth_seed": 20260806
      },
      {
        "comparison_status": "IDENTICAL_TARGET_RESULT",
        "control": "C07",
        "enumeration": {
          "baseline_all_candidates": {
            "bam": 227,
            "delta": -8851,
            "direct": 9078
          },
          "baseline_gene_pair_candidates": {
            "bam": 0,
            "delta": -1,
            "direct": 1
          },
          "spiked_all_candidates": {
            "bam": 228,
            "delta": -8851,
            "direct": 9079
          },
          "spiked_gene_pair_candidates": {
            "bam": 1,
            "delta": -1,
            "direct": 2
          }
        },
        "exact_caller_result": {
          "baseline_target_window_matches": 0,
          "fusion_support_fraction": 0.080163,
          "hard_filters": [],
          "left_error_bp": 2,
          "right_error_bp": 2,
          "score": 1.0,
          "soft_filters": [
            "auto_reporting_disabled",
            "unvalidated_scorer",
            "missing_pon",
            "unverified_duplicate_processing"
          ],
          "spanning_pairs": 11,
          "spanning_pairs_unique": 11,
          "spiked_target_window_matches": 1,
          "split_reads": 80,
          "split_reads_unique": 52,
          "target_detected": true,
          "target_reportable": false,
          "target_window_ambiguous": false,
          "tier": "REVIEW",
          "total_support": 63
        },
        "fusion": "CD74-ROS1",
        "truth_identity_verified": true,
        "truth_seed": 20260807
      }
    ],
    "identical_fields": [
      "target_detected",
      "target_reportable",
      "left_error_bp",
      "right_error_bp",
      "tier",
      "score",
      "split_reads",
      "split_reads_unique",
      "spanning_pairs",
      "spanning_pairs_unique",
      "total_support",
      "fusion_support_fraction",
      "baseline_target_window_matches",
      "spiked_target_window_matches",
      "target_window_ambiguous",
      "hard_filters",
      "soft_filters"
    ],
    "interpretation": "Detection, reportability, breakpoint error, tier, score, split/spanning support, total support, and matched target-window counts are identical for all seven controls. Full-reference BAM ingestion enumerates far fewer broad candidates and removes baseline target-gene-pair candidates, while retaining exactly one spiked target-window candidate."
  },
  "created_utc": "2026-07-31T22:25:01.808508+00:00",
  "headline": "All seven target outcomes are identical after full-reference BWA-MEM alignment; only broad candidate enumeration changed.",
  "public_safety": {
    "laboratory_read_groups_exported": false,
    "local_paths_exported": false,
    "pseudonymous_controls_only": true,
    "qnames_exported": false
  },
  "schema": "spikeforge-direct-fastq-vs-full-reference-bam-v1",
  "sources": {
    "direct_fastq_table": {
      "name": "fastq_control_results.csv",
      "sha256": "4138c1a40ec334a710856ec6992acbf66713c5401335500e7ba116f251a5809d"
    },
    "full_reference_bam_table": {
      "name": "full_reference_control_results.csv",
      "sha256": "dd4ec81269c5881ca7d04602b9ced30df24e387d6a3925024a688317f9fddbf4"
    }
  },
  "status": "PASS"
}