{ "artifact_manifest": "benchmark.manifest.json", "claims_boundary": "Hand-constructed aligned-BAM regression fixtures, including conditionally topped-up controls, verify deterministic software behavior only. Their coupled alignment fields were not jointly produced by a pinned production aligner against the intended full reference, so they are not synthetic-read validation. They establish neither analytical nor clinical sensitivity, specificity, PPV, NPV, limit of blank, LoD95, precision, reproducibility, or transportability.", "cohort": [ { "bam": "synthetic-inputs/FIT_01.bam", "realized_truth_alleles": 1, "role": "fixed_union_PoN_fit_only_excluded_from_primary_endpoints", "sample": "FIT_01", "split": "fit", "truth_manifest": "synthetic-inputs/FIT_01.bam.truth.json" }, { "bam": "synthetic-inputs/FIT_02.bam", "realized_truth_alleles": 1, "role": "fixed_union_PoN_fit_only_excluded_from_primary_endpoints", "sample": "FIT_02", "split": "fit", "truth_manifest": "synthetic-inputs/FIT_02.bam.truth.json" }, { "bam": "synthetic-inputs/CALIBRATION_NEGATIVE.bam", "realized_truth_alleles": 0, "role": "negative_check_no_threshold_fitting", "sample": "CALIBRATION_NEGATIVE", "split": "calibration", "truth_manifest": "synthetic-inputs/CALIBRATION_NEGATIVE.bam.truth.json" }, { "bam": "synthetic-inputs/DEVELOPMENT_POSITIVE.bam", "realized_truth_alleles": 4, "role": "transparent_development_positive", "sample": "DEVELOPMENT_POSITIVE", "split": "development", "truth_manifest": "synthetic-inputs/DEVELOPMENT_POSITIVE.bam.truth.json" }, { "bam": "synthetic-inputs/LOCKBOX_POSITIVE.bam", "realized_truth_alleles": 8, "role": "deterministic_synthetic_lockbox_label_not_blinded_clinical_lockbox", "sample": "LOCKBOX_POSITIVE", "split": "lockbox", "truth_manifest": "synthetic-inputs/LOCKBOX_POSITIVE.bam.truth.json" }, { "bam": "synthetic-inputs/LOCKBOX_SPIKEFORGE.bam", "realized_truth_alleles": 3, "role": "external_generator_interoperability_control", "sample": "LOCKBOX_SPIKEFORGE", "split": "lockbox", "truth_manifest": "synthetic-inputs/LOCKBOX_SPIKEFORGE.truth/manifest.json" }, { "bam": "synthetic-inputs/STRESS_FFPE_LOW_DEPTH.bam", "realized_truth_alleles": 8, "role": "simplified_FFPE_and_depth_stress", "sample": "STRESS_FFPE_LOW_DEPTH", "split": "stress", "truth_manifest": "synthetic-inputs/STRESS_FFPE_LOW_DEPTH.bam.truth.json" }, { "bam": "synthetic-inputs/CHANGED_ASSAY_MGI.bam", "realized_truth_alleles": 4, "role": "platform_label_transport_challenge", "sample": "CHANGED_ASSAY_MGI", "split": "changed-assay", "truth_manifest": "synthetic-inputs/CHANGED_ASSAY_MGI.bam.truth.json" }, { "bam": "synthetic-inputs/UMI_CONSENSUS_POSITIVE.bam", "realized_truth_alleles": 1, "role": "explicit_umi_family_end_to_end_control", "sample": "UMI_CONSENSUS_POSITIVE", "split": "development", "truth_manifest": "synthetic-inputs/UMI_CONSENSUS_POSITIVE.bam.truth.json" }, { "bam": "synthetic-inputs/EXPLICIT_NO_CALL_EDGE.bam", "realized_truth_alleles": 1, "role": "prespecified_off_target_no_call_denominator_control", "sample": "EXPLICIT_NO_CALL_EDGE", "split": "stress", "truth_manifest": "synthetic-inputs/EXPLICIT_NO_CALL_EDGE.evaluation-truth.json" } ], "comparators": [ { "name": "transparent_pileup_baseline", "requirements": "same normalized truth, regions, samples, and callability", "status": "NOT_RUN" }, { "name": "GATK_Mutect2_or_HaplotypeCaller_as_assay_appropriate", "requirements": "pinned container/digest and identical evaluation mask", "status": "NOT_RUN" }, { "name": "Strelka2_or_LoFreq_as_assay_appropriate", "requirements": "pinned container/digest and identical evaluation mask", "status": "NOT_RUN" } ], "control_generation_accounting": { "aggregation_unit": "allele_primary_unit_observations; summed counts are not unique physical fragments across alleles", "all_declared_simulator_floors_satisfied": true, "interpretation": "forced_top_up_primary_units are disclosed deterministic control construction; caller recovery from these controls is not an analytical or clinical sensitivity estimate", "schema": "mutationsieve.benchmark-control-generation-accounting.v1", "simulator": { "declared_minimum_primary_units": 75, "floor_prioritized_primary_units": 75, "forced_top_up_primary_units": 67, "ordinary_selected_floor_contributions": 8, "ordinary_selection_events": 131, "positive_truth_alleles": 25, "primary_units_realized": 192, "truth_alleles": 25, "truth_alleles_with_declared_floor": 25, "truth_alleles_with_forced_top_up": 24 }, "simulator_runs_in_realization_gate": 6, "spikeforge_truth_alleles": 3 }, "decision_rule": "tier != REJECT; all rejected candidates retained in audit outputs", "design": { "calibration_changes_thresholds": false, "confidence_intervals": "two-sided Clopper-Pearson exact", "control_realization_policy": "positive MutationSieve-simulator controls declare a minimum carrying-primary-unit floor; ordinary and forced units are separately disclosed and are not sensitivity evidence", "fit_and_evaluation_are_disjoint": true, "fit_fragments_per_sample": 1600, "generator": "MutationSieve hand-constructed aligned-BAM fixture generator", "ordinary_fragments_per_sample": 2400, "primary_denominator": "all realized truth alleles, including no-call regions", "reportable_tiers_enabled": false, "stress_fragments_per_sample": 1500, "truth_match": "record-exact normalized metrics plus separately labeled bounded MNV/component-substitution representation equivalence" }, "environment": { "architecture": "AMD64", "dependencies": { "numpy": "2.5.1", "scipy": "1.18.0" }, "limitation": "observational record, not a lockfile, container digest, or guarantee of binary reproducibility", "locked_environment": false, "mutationsieve": "0.1.0.dev1", "operating_system": "Windows", "os_release": "10", "purpose": "observed_software_verification_environment", "python": "3.14.6", "python_implementation": "CPython", "schema": "mutationsieve.environment.v1" }, "environment_json": "environment.json", "failed_hypotheses": [], "hypothesis_register": [ { "hypothesis": "At least one designed SNV is called by exact normalized allele match.", "id": "SWV-REP-SNV", "observed": { "true_positives": 10, "truth_total": 10 }, "prespecified_gate": "true_positives >= 1 when class denominator > 0", "scope": "synthetic software representation only", "status": "PASSED" }, { "hypothesis": "At least one designed MNV is called by exact normalized allele match.", "id": "SWV-REP-MNV", "observed": { "true_positives": 2, "truth_total": 2 }, "prespecified_gate": "true_positives >= 1 when class denominator > 0", "scope": "synthetic software representation only", "status": "PASSED" }, { "hypothesis": "At least one designed INS is called by exact normalized allele match.", "id": "SWV-REP-INS", "observed": { "true_positives": 7, "truth_total": 8 }, "prespecified_gate": "true_positives >= 1 when class denominator > 0", "scope": "synthetic software representation only", "status": "PASSED" }, { "hypothesis": "At least one designed DEL is called by exact normalized allele match.", "id": "SWV-REP-DEL", "observed": { "true_positives": 7, "truth_total": 7 }, "prespecified_gate": "true_positives >= 1 when class denominator > 0", "scope": "synthetic software representation only", "status": "PASSED" }, { "hypothesis": "At least one designed COMPLEX is called by exact normalized allele match.", "id": "SWV-REP-COMPLEX", "observed": { "true_positives": 2, "truth_total": 2 }, "prespecified_gate": "true_positives >= 1 when class denominator > 0", "scope": "synthetic software representation only", "status": "PASSED" }, { "hypothesis": "The synthetic calibration negative has no selected positive calls.", "id": "SWV-CAL-FP", "observed": { "false_positives": 0, "samples": 1 }, "prespecified_gate": "false_positives == 0", "scope": "single deterministic synthetic negative; not a limit-of-blank study", "status": "PASSED" }, { "hypothesis": "The prespecified off-target truth remains in the intention-to-test denominator as a no-call miss.", "id": "SWV-CALLABILITY", "observed": { "challenge_samples": 1, "false_negatives_intention_to_test": 1, "sample_statuses": [ "PARTIAL_COVERAGE_NO_CALL" ], "truth_interval_not_callable_misses": 1, "truth_no_call": 1 }, "prespecified_gate": "one challenge; truth_no_call == 1; one intention-to-test miss explicitly caused by a non-callable interval; sample status is a no-call", "scope": "explicit no-call denominator behavior", "status": "PASSED" }, { "display_name": "Representation-equivalent control recovery", "hypothesis": "Every realized allele in the hand-constructed aligned-BAM fixture, except the one prespecified off-target no-call challenge, is selected as a representation-equivalent call.", "id": "SWV-REPRESENTATION-RECALL", "observed": { "false_negatives_intention_to_test": 1, "prespecified_no_call_truth": 1, "true_positives_intention_to_test": 28, "truth_total_intention_to_test": 29 }, "prespecified_gate": "true_positives_intention_to_test == truth_total_intention_to_test - prespecified_no_call_truth, and all misses are that challenge", "scope": "deterministic representation-equivalent control recovery; not synthetic-read validation or analytical/clinical sensitivity", "status": "PASSED" }, { "hypothesis": "The required hash-identified SpikeForge control is generated and its output-integrity verification passes.", "id": "SWV-SPIKEFORGE-INTEROPERABILITY", "observed": { "status": "PASS", "verification": { "added": 0, "fields_touched": [ "cigar", "qual", "seq", "tag:NM" ], "header_identical": false, "header_note": "header differs only by one appended SpikeForge @PG record", "header_ok": true, "identical": 4747, "input_records": 4800, "modified": 53, "ok": true, "output_records": 4800, "removed": 0, "summary": "[PASS] in=4800 out=4800 identical=4747 modified=53 added=0 removed=0 unexpected=0", "unexpected": [] } }, "prespecified_gate": "control.status == PASS", "scope": "cross-project software interoperability", "status": "PASSED" }, { "hypothesis": "The explicit UMI control uses UMI families as its primary unit.", "id": "SWV-UMI-CONSENSUS", "observed": { "primary_analysis_units": [ "explicit_umi_family" ], "samples": 1 }, "prespecified_gate": "one UMI control and explicit_umi_family in primary_analysis_units", "scope": "explicit UMI-family end-to-end software behavior", "status": "PASSED" }, { "hypothesis": "An MGI-labelled case cannot load an Illumina PoN.", "id": "SWV-CHANGED-ASSAY-FAIL-CLOSED", "observed": { "expected": "strict PoN platform identity mismatch", "observed_error": "PoN compatibility identity mismatch (sequencing_platforms: PoN=['ILLUMINA'], runtime=['MGI'])", "status": "PASSED" }, "prespecified_gate": "strict incompatible PoN attempt raises identity mismatch", "scope": "declared-platform resource compatibility", "status": "PASSED" }, { "display_name": "SpikeForge structural edit-output integrity", "hypothesis": "SpikeForge-edited aligned records pass the native structural-field and local-distribution audit.", "id": "SWV-SPIKEFORGE-REALISM", "observed": { "checked_fields": [ "NM", "RG", "TLEN", "mapq", "mean base quality", "read length", "soft-clipped bases" ], "counts": { "background": 3567, "edited": 96, "planted": 0 }, "findings": [ { "detail": "median 1.0 vs 0.0 in nearby real reads (KS D=0.55, p=7.5e-26) -- expected: the edit adds a mismatch", "field": "NM", "group": "edited", "severity": "expected", "stat": 0.5520833333333333 } ], "ok": true, "skipped": "", "summary": "[PASS] edited=96 planted=0 background=3567 errors=0 separable=0 shifted=0" }, "prespecified_gate": "external_realism_audit.ok == true", "scope": "structural edit-output integrity/distribution check; not alignment realism, synthetic-read validation, or biological performance", "status": "PASSED" }, { "hypothesis": "Within every realization-gated control run, every designed synthetic allele is realized in at least one primary unit.", "id": "SWV-CONTROL-REALIZATION", "observed": { "control_generation_accounting": { "aggregation_unit": "allele_primary_unit_observations; summed counts are not unique physical fragments across alleles", "all_declared_simulator_floors_satisfied": true, "interpretation": "forced_top_up_primary_units are disclosed deterministic control construction; caller recovery from these controls is not an analytical or clinical sensitivity estimate", "schema": "mutationsieve.benchmark-control-generation-accounting.v1", "simulator": { "declared_minimum_primary_units": 75, "floor_prioritized_primary_units": 75, "forced_top_up_primary_units": 67, "ordinary_selected_floor_contributions": 8, "ordinary_selection_events": 131, "positive_truth_alleles": 25, "primary_units_realized": 192, "truth_alleles": 25, "truth_alleles_with_declared_floor": 25, "truth_alleles_with_forced_top_up": 24 }, "simulator_runs_in_realization_gate": 6, "spikeforge_truth_alleles": 3 }, "designed_truth_alleles": 28, "every_included_run_complete": true, "realized_truth_alleles": 28, "runs": [ { "complete": true, "designed_truth_alleles": 0, "realized_truth_alleles": 0, "sample": "CALIBRATION_NEGATIVE" }, { "complete": true, "designed_truth_alleles": 4, "realized_truth_alleles": 4, "sample": "DEVELOPMENT_POSITIVE" }, { "complete": true, "designed_truth_alleles": 8, "realized_truth_alleles": 8, "sample": "LOCKBOX_POSITIVE" }, { "complete": true, "designed_truth_alleles": 3, "realized_truth_alleles": 3, "sample": "LOCKBOX_SPIKEFORGE" }, { "complete": true, "designed_truth_alleles": 8, "realized_truth_alleles": 8, "sample": "STRESS_FFPE_LOW_DEPTH" }, { "complete": true, "designed_truth_alleles": 4, "realized_truth_alleles": 4, "sample": "CHANGED_ASSAY_MGI" }, { "complete": true, "designed_truth_alleles": 1, "realized_truth_alleles": 1, "sample": "UMI_CONSENSUS_POSITIVE" } ] }, "prespecified_gate": "for every included run: realized_truth_alleles == designed_truth_alleles", "scope": "control-generation adequacy, separate from caller performance", "status": "PASSED" } ], "independent_control_register": [ { "edited_reads": 53, "executed_module_origins": { "spikeforge": "__init__.py", "spikeforge.bamio": "bamio.py", "spikeforge.bgzf": "bgzf.py", "spikeforge.fastqspike": "fastqspike.py", "spikeforge.fusion": "fusion.py", "spikeforge.mdtag": "mdtag.py", "spikeforge.mutate": "mutate.py", "spikeforge.pipeline": "pipeline.py", "spikeforge.realism": "realism.py", "spikeforge.refseq": "refseq.py", "spikeforge.truth": "truth.py", "spikeforge.verify": "verify.py" }, "independence_statement": "mutation planting and output verification use the separately implemented SpikeForge source selected from sibling_repository; the unmutated hand-constructed aligned-BAM baseline and compact reference are shared inputs, and no pinned production aligner is run", "name": "SpikeForge small-variant control", "realism": { "checked_fields": [ "NM", "RG", "TLEN", "mapq", "mean base quality", "read length", "soft-clipped bases" ], "counts": { "background": 3567, "edited": 96, "planted": 0 }, "findings": [ { "detail": "median 1.0 vs 0.0 in nearby real reads (KS D=0.55, p=7.5e-26) -- expected: the edit adds a mismatch", "field": "NM", "group": "edited", "severity": "expected", "stat": 0.5520833333333333 } ], "ok": true, "skipped": "", "summary": "[PASS] edited=96 planted=0 background=3567 errors=0 separable=0 shifted=0" }, 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{ "hypothesis": "At least one designed COMPLEX is called by exact normalized allele match.", "id": "SWV-REP-COMPLEX", "observed": { "true_positives": 2, "truth_total": 2 }, "prespecified_gate": "true_positives >= 1 when class denominator > 0", "scope": "synthetic software representation only", "status": "PASSED" }, { "hypothesis": "The synthetic calibration negative has no selected positive calls.", "id": "SWV-CAL-FP", "observed": { "false_positives": 0, "samples": 1 }, "prespecified_gate": "false_positives == 0", "scope": "single deterministic synthetic negative; not a limit-of-blank study", "status": "PASSED" }, { "hypothesis": "The prespecified off-target truth remains in the intention-to-test denominator as a no-call miss.", "id": "SWV-CALLABILITY", "observed": { "challenge_samples": 1, "false_negatives_intention_to_test": 1, "sample_statuses": [ "PARTIAL_COVERAGE_NO_CALL" ], "truth_interval_not_callable_misses": 1, "truth_no_call": 1 }, "prespecified_gate": "one challenge; truth_no_call == 1; one intention-to-test miss explicitly caused by a non-callable interval; sample status is a no-call", "scope": "explicit no-call denominator behavior", "status": "PASSED" }, { "display_name": "Representation-equivalent control recovery", "hypothesis": "Every realized allele in the hand-constructed aligned-BAM fixture, except the one prespecified off-target no-call challenge, is selected as a representation-equivalent call.", "id": "SWV-REPRESENTATION-RECALL", "observed": { "false_negatives_intention_to_test": 1, "prespecified_no_call_truth": 1, "true_positives_intention_to_test": 28, "truth_total_intention_to_test": 29 }, "prespecified_gate": "true_positives_intention_to_test == truth_total_intention_to_test - prespecified_no_call_truth, and all misses are that challenge", "scope": "deterministic representation-equivalent control recovery; not synthetic-read validation or analytical/clinical sensitivity", "status": "PASSED" }, { "hypothesis": "The required hash-identified SpikeForge control is generated and its output-integrity verification passes.", "id": "SWV-SPIKEFORGE-INTEROPERABILITY", "observed": { "status": "PASS", "verification": { "added": 0, "fields_touched": [ "cigar", "qual", "seq", "tag:NM" ], "header_identical": false, "header_note": "header differs only by one appended SpikeForge @PG record", "header_ok": true, "identical": 4747, "input_records": 4800, "modified": 53, "ok": true, "output_records": 4800, "removed": 0, "summary": "[PASS] in=4800 out=4800 identical=4747 modified=53 added=0 removed=0 unexpected=0", "unexpected": [] } }, "prespecified_gate": "control.status == PASS", "scope": "cross-project software interoperability", "status": "PASSED" }, { "hypothesis": "The explicit UMI control uses UMI families as its primary unit.", "id": "SWV-UMI-CONSENSUS", "observed": { "primary_analysis_units": [ "explicit_umi_family" ], "samples": 1 }, "prespecified_gate": "one UMI control and explicit_umi_family in 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