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"unassigned_units": 46 }, "index_unassigned_fraction": 0.017767477790652762, "insert_median_bp": 146, "library_units": 2589, "mappable_library_units": 2586, "mapped_primary": 2543, "mean_read_q": 19.455785090553128, "metric_schema_version": 3, "metric_settings": { "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" }, "mitochondrial_chromosomes_used": [ "chrM" ], "mitochondrial_fraction": 0.0009103322712790169, "mycoplasma_qualifying_fraction": 0.0, "mycoplasma_qualifying_loci": 0, "mycoplasma_qualifying_reads": 0, "mycoplasma_screen": { "interpretation": "Opportunistic competitive-alignment screen; a negative result at shallow depth is not a contamination-free certificate.", "minimum_screened_reads": 500, "qualifying_fraction": 0.0, "qualifying_loci": 0, "qualifying_reads": 0, "screened_reads": 2586, "status": "NOT_DETECTED_AT_THIS_DEPTH" }, "mycoplasma_screened_reads": 2586, "mycoplasma_status": "NOT_DETECTED_AT_THIS_DEPTH", "outer_complete_unit_rate": 0.8230977211278486, "outer_complete_units": 2131, "primary_chromosomes_used": [ "chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX" ], "primary_mapping_rate": 0.9833720030935809, "probable_adapter_dimer_units": 0, "raw_median_bp": 276.0, "raw_n50_bp": 294, "raw_reads": 2936, "raw_structure_dimer_rate": 0.0010217983651226157, "reference_assembly": "hg38", "sample": "HL240", "sequencing_yield_call": "pass", "short_unmapped_units": 0, "spike_in_declared": false, "spike_in_fraction": 0.0, "spike_in_fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "spike_in_label": "No candidate signal", "spike_in_reads": 0, "spike_in_screen": { "assignment_counts": { "ambiguous_or_unassigned": 605, "host": 1981 }, "candidates": { "d_melanogaster": { "fraction": 0.0, "fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "label": "Drosophila melanogaster", "loci": 0, "reads": 0, "role": "spikein_candidate", "status": "NOT_DETECTED" }, "e_coli": { "fraction": 0.0, "fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "label": "Escherichia coli", "loci": 0, "reads": 0, "role": "spikein_candidate", "status": "NOT_DETECTED" }, "lambda": { "fraction": 0.0, "fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "label": "Lambda phage", "loci": 0, "reads": 0, "role": "sequencing_control", "status": "NOT_DETECTED" }, "phix": { "fraction": 0.0, "fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "label": "PhiX174", "loci": 0, "reads": 0, "role": "sequencing_control", "status": "NOT_DETECTED" }, "s_cerevisiae": { "fraction": 0.0, "fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "label": "Saccharomyces cerevisiae", "loci": 0, "reads": 0, "role": "spikein_candidate", "status": "NOT_DETECTED" }, "s_pombe": { "fraction": 0.0, "fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "label": "Schizosaccharomyces pombe", "loci": 0, "reads": 0, "role": "spikein_candidate", "status": "NOT_DETECTED" } }, "command": [ "/path/to/bowtie2", "--very-sensitive-local", "-p", "4", "-x", "/path/to/index", "-U", "/path/to/HL240.inserts.fastq.gz" ], "database_manifest": "/path/to/d2aba8b035c32cdecb131b1809d757479200c65ee888a8dc001abde9636a6b59.json", "database_source": "/path/to/manifest.json", "declared_spike_in": false, "fraction_ci95": [ 1.0842021724855044e-19, 0.0014832795295675614 ], "host_reference": "hg38", "interpretation": "Candidate foreign-sequence signal, not proof that spike-in was intentionally added. Experimental spike-in intent must be established from metadata; positive signals require investigation. Zero hits do not establish absence, and the binomial bound assumes independent inserts and perfect detectability. Host and candidate genomes plus Mollicutes/bacterial decoys compete in one alignment.", "label": "Common spike-in candidates", "mode": "auto", "parameters": { "mapq": 20, "minimum_aligned_bp": 80, "minimum_identity": 0.85, "minimum_query_coverage": 0.8, "minimum_score_margin": 10 }, "qualifying_fraction": 0.0, "qualifying_reads": 0, "screened_reads": 2586, "status": "NOT_DETECTED", "zero_hit_upper95": 0.0011577717523688635 }, "spike_in_screened_reads": 2586, "spike_in_species_counts": {}, "spike_in_status": "NOT_DETECTED", "sub_libraries": [], "units_per_complete_read": 1.004266873545384, "unreconstructed_probable_dimer_reads": 8, "usable_fragment_rate": 0.8488012374323279, "usable_fragments": 2195, "metric_profile": "ont_native", "metric_definition_version": "2026.09.10" }