evidence_track claim_role status model_or_workflow dataset_or_suite metric estimate ci_lower ci_upper numerator denominator unit replicates source limitation source_run_id source_standard_table source_standard_table_sha256 source_artifact source_artifact_sha256 agent_operability primary_local_model_benchmark pending_new_run local_model_family_pairs ABI-Bench causal_core_v0_8 G3_minus_G1 fraction_point_delta ABI-Bench evaluation_suites.yaml All pre-existing benchmark outcomes were excluded; populate only after a clean preregistered rerun NA NA NA NA NA agent_operability primary_local_model_benchmark pending_new_run local_model_family_pairs ABI-Bench causal_core_v0_8 G3_minus_G2 fraction_point_delta ABI-Bench evaluation_suites.yaml All pre-existing benchmark outcomes were excluded; populate only after a clean preregistered rerun NA NA NA NA NA agent_operability primary_local_model_benchmark pending_new_run local_model_family_pairs ABI-Bench causal_core_v0_8 G3_minus_G4 fraction_point_delta ABI-Bench evaluation_suites.yaml All pre-existing benchmark outcomes were excluded; G4 isolates callable control from information volume NA NA NA NA NA agent_operability hidden_local_model_robustness pending_new_run local_model_family_pairs ABI-Bench hidden_robustness_v0_9 diagnostic_accuracy_delta fraction_point_delta ABI-Bench evaluation_suites.yaml Populate only from hidden fixtures after the public-suite design and model registry are frozen NA NA NA NA NA biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated steps_completed_fraction 1.0 26 26 fraction 1 /docs/zh/real_data_validation_datasets.md Resume statuses prove workflow completion, not independent recomputation of every step legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated genes_tested 16019 16019 genes 1 /docs/zh/real_data_validation_datasets.md STAR/featureCounts/DESeq2 differs from the original TopHat/Cufflinks/Cuffdiff workflow in alignment, counting, gene aggregation, dispersion estimation, and multiple-testing implementation legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated matched_genes_for_effect_comparison 13148 13148 genes 1 /docs/zh/real_data_validation_datasets.md Only genes mappable between ABI and GEO result tables are compared legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated abi_mapped_significant_genes 4013 4013 genes 1 /docs/zh/real_data_validation_datasets.md ABI significant genes among the mapped comparison set; differs from the total tested-gene count legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated geo_mapped_significant_genes 304 304 genes 1 /docs/zh/real_data_validation_datasets.md GEO Cuffdiff significant genes among the mapped comparison set legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated log2fc_spearman_rho 0.9613 13148 correlation 1 /docs/zh/real_data_validation_datasets.md GEO Cuffdiff effect sign was reversed before comparison to express Dex relative to untreated legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated effect_direction_concordance 0.9103 13148 fraction 1 /docs/zh/real_data_validation_datasets.md Agreement is directional and does not imply identical p-values or FDR legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated sentinel_gene_direction_concordance 1.0 7 7 fraction 1 /docs/zh/real_data_validation_datasets.md Sentinel genes were preregistered; this is not a genome-wide accuracy estimate legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated significant_gene_overlap 304 304 genes 1 /docs/zh/real_data_validation_datasets.md Significance thresholds operate on different aligner/count/statistical pipelines legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible rnaseq_expression GSE52778 Airway Dex versus untreated significant_set_jaccard 0.0758 304 fraction 1 /docs/zh/real_data_validation_datasets.md Low overlap is expected under different alignment/counting/statistical pipelines; do not use as the sole validity endpoint legacy-sha256:fdd7aeb25111531666c3bc26ff49044251642ee373d7f46eb6edbd167f704303 downloads/rnaseq_retry5/tables/differential_expression.tsv 9d69ba0a30e4bb60b8fb65c1d1988c570ea2c24ec8c589dc27aa97a8ee0ce14f docs/paper_examples/airway_metrics.tsv 69123fa7cea621bd92bb84204509bfef40feaa9c5922f5178bf96735202764fc biological_validation running_example claim_eligible wgs_bacteria PRJNA286158 ST93 MRSA steps_completed_fraction 1.0 30 30 fraction 1 /docs/zh/real_data_validation_datasets.md Execution completion does not cover the absent core-SNP analysis legacy-sha256:313338bb1f9f64e6ebea5e0334002457aebf0141d6d86f56ea3228275d241bbf downloads/wgs_st93_mrsa_retry/tables/mlst_profile.tsv e2239952ca1b8266f04ce4351b20a0fd490a009283ce0cf692006e329dae6d15 downloads/wgs_st93_mrsa_retry/tables/mlst_profile.tsv e2239952ca1b8266f04ce4351b20a0fd490a009283ce0cf692006e329dae6d15 biological_validation running_example claim_eligible wgs_bacteria PRJNA286158 ST93 MRSA ST93_concordance 1.0 6 6 fraction 1 /docs/zh/real_data_validation_datasets.md Six-isolate study-specific validation; not a general MLST accuracy estimate legacy-sha256:313338bb1f9f64e6ebea5e0334002457aebf0141d6d86f56ea3228275d241bbf downloads/wgs_st93_mrsa_retry/tables/mlst_profile.tsv e2239952ca1b8266f04ce4351b20a0fd490a009283ce0cf692006e329dae6d15 downloads/wgs_st93_mrsa_retry/tables/mlst_profile.tsv e2239952ca1b8266f04ce4351b20a0fd490a009283ce0cf692006e329dae6d15 biological_validation running_example claim_eligible wgs_bacteria PRJNA286158 ST93 MRSA mecA_concordance 1.0 6 6 fraction 1 /docs/zh/real_data_validation_datasets.md Each call had 100% amino-acid coverage and identity; broader AMR phenotype concordance was not assessed legacy-sha256:313338bb1f9f64e6ebea5e0334002457aebf0141d6d86f56ea3228275d241bbf downloads/wgs_st93_mrsa_retry/tables/amr_profile.tsv 5a5f5719bbbecc43f07496c04a6d01fa7a0f18742d5e6d15bfb51dc3daee291a downloads/wgs_st93_mrsa_retry/tables/amr_profile.tsv 5a5f5719bbbecc43f07496c04a6d01fa7a0f18742d5e6d15bfb51dc3daee291a biological_validation running_example claim_eligible wgs_bacteria PRJNA286158 ST93 MRSA amr_standard_table_rows 145 145 rows 1 /docs/zh/real_data_validation_datasets.md Rows are tool calls and must not be interpreted as 145 unique resistance determinants legacy-sha256:313338bb1f9f64e6ebea5e0334002457aebf0141d6d86f56ea3228275d241bbf downloads/wgs_st93_mrsa_retry/tables/amr_profile.tsv 5a5f5719bbbecc43f07496c04a6d01fa7a0f18742d5e6d15bfb51dc3daee291a downloads/wgs_st93_mrsa_retry/tables/amr_profile.tsv 5a5f5719bbbecc43f07496c04a6d01fa7a0f18742d5e6d15bfb51dc3daee291a biological_validation running_example claim_eligible spandx_v2_6_paper_track PRJNA286158+PRJEB3144+PRJNA232112 ST93 MRSA paper_spandx_pairwise_snp_min 7 7 snps 1 /docs/paper_examples/wgs_snp_track_comparison.tsv Strict comparison with the original SPANDx v2.6 toolchain on the full 82-sample paper context; published minimum is 7 evidence-sha256:f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2:wgs-snp-comparison docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 biological_validation running_example claim_eligible spandx_v2_6_paper_track PRJNA286158+PRJEB3144+PRJNA232112 ST93 MRSA paper_spandx_pairwise_snp_max 60 60 snps 1 /docs/paper_examples/wgs_snp_track_comparison.tsv Strict comparison with the original SPANDx v2.6 toolchain on the full 82-sample paper context; published maximum is 60 evidence-sha256:f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2:wgs-snp-comparison docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 biological_validation running_example claim_eligible spandx_v2_6_paper_track PRJNA286158+PRJEB3144+PRJNA232112 ST93 MRSA paper_spandx_pairwise_snp_median 47 snps 1 /docs/paper_examples/wgs_snp_track_comparison.tsv Median across the 15 six-isolate pairs; published mean is 44 evidence-sha256:f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2:wgs-snp-comparison docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 biological_validation running_example claim_eligible spandx_v2_6_paper_track PRJNA286158+PRJEB3144+PRJNA232112 ST93 MRSA paper_spandx_pairwise_range_match 1.0 15 15 fraction 1 /docs/paper_examples/wgs_snp_track_comparison.tsv All 15 six-isolate pairwise distances fall inside the published 7-60 range; this is a paper-method distance-endpoint recovery, not a full paper-exact outbreak reproduction; the ABI plugin itself ships no core-SNP module evidence-sha256:f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2:wgs-snp-comparison docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 docs/paper_examples/wgs_snp_pairwise_distances.tsv f765e2b88edaaf3dbbff021d78a142e955454044e588eb2b6a545fb0881b2fe2 biological_validation running_example claim_eligible abi_bcftools_track PRJNA286158 ST93 MRSA abi_bcftools_pairwise_snp_min 10 10 snps 1 /docs/paper_examples/wgs_snp_track_comparison.tsv ABI-adjacent BWA mem plus bcftools haploid joint calling; 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not paper-exact; unmatched predictions are not necessarily biological false positives legacy-sha256:f8a8e13c360ac19267a23fbfa240e40f9651b053389fc0bd0c7db492dcdc4c9f docs/zh/figures/data/scapp_paper_method_v2_20260724/evidence_match_table.tsv 795ee60b4b3062ceb809ffc7b8421a8a81971f01710cd7dd13e0813143e6c260 docs/zh/figures/data/scapp_paper_method_v2_20260724/score_summary.json 1e4f4c398fed7ce14b6adc0d7656bd848d9531ec9eefa092398dccb62cff7133 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 SCAPP plasmidome paper_method_recall 0.7272727272727273 64 88 fraction 1 /docs/zh/real_data_validation_datasets.md Paper-method reconstruction against the official 14,739-record PLSDB archive; not paper-exact; 88 truth references were reconstructed by the independent K127 assembly legacy-sha256:f8a8e13c360ac19267a23fbfa240e40f9651b053389fc0bd0c7db492dcdc4c9f docs/zh/figures/data/scapp_paper_method_v2_20260724/evidence_match_table.tsv 795ee60b4b3062ceb809ffc7b8421a8a81971f01710cd7dd13e0813143e6c260 docs/zh/figures/data/scapp_paper_method_v2_20260724/score_summary.json 1e4f4c398fed7ce14b6adc0d7656bd848d9531ec9eefa092398dccb62cff7133 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 SCAPP plasmidome paper_method_f1 0.138328530259366 fraction 1 /docs/zh/real_data_validation_datasets.md Harmonic mean of paper-method precision 12/157 and recall 64/88; not paper-exact legacy-sha256:f8a8e13c360ac19267a23fbfa240e40f9651b053389fc0bd0c7db492dcdc4c9f docs/zh/figures/data/scapp_paper_method_v2_20260724/evidence_match_table.tsv 795ee60b4b3062ceb809ffc7b8421a8a81971f01710cd7dd13e0813143e6c260 docs/zh/figures/data/scapp_paper_method_v2_20260724/score_summary.json 1e4f4c398fed7ce14b6adc0d7656bd848d9531ec9eefa092398dccb62cff7133 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 SCAPP original reproduction steps_completed_fraction 1.0 1 1 fraction 1 /docs/zh/real_data_validation_datasets.md SPAdes 3.13.1 meta -k 21,33,55,77 assembly followed by original SCAPP -k 77 evidence-sha256:138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0:scapp-original-comparison downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 SCAPP original reproduction original_scapp_predictions 102 102 predictions 1 /docs/zh/real_data_validation_datasets.md Original SCAPP defaults on SRR11038083 paper protocol evidence-sha256:138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0:scapp-original-comparison downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 SCAPP original reproduction original_scapp_precision 0.12745098039215685 13 102 fraction 1 /docs/zh/real_data_validation_datasets.md Against paper-method gold standard from PLSDB 2018-12-05; not paper-exact evidence-sha256:138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0:scapp-original-comparison downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 SCAPP original reproduction original_scapp_recall 0.8160919540229885 71 87 fraction 1 /docs/zh/real_data_validation_datasets.md Against paper-method gold standard from PLSDB 2018-12-05; not paper-exact evidence-sha256:138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0:scapp-original-comparison downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 SCAPP original reproduction original_scapp_f1 0.22047056013376326 fraction 1 /docs/zh/real_data_validation_datasets.md Harmonic mean of precision 13/102 and recall 71/87 evidence-sha256:138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0:scapp-original-comparison downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 ABI SCAPP node steps_completed_fraction 1.0 5 5 fraction 1 /docs/zh/real_data_validation_datasets.md ABI metagenomic_plasmid workflow: qc_fastp, assembly_metaspades, genomad, plasmid_consensus, scapp legacy-sha256:789f08d8664e214a29d7bd62b97873458877b42d46c691816e3e1d9157e4a482 downloads/abi_scapp/tables/plasmid_predictions.tsv 56eaea090d98390bbecc5153891865b36b2d12b59f6ad844ce8c149b198644ee downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 ABI SCAPP node abi_scapp_predictions 103 103 predictions 1 /docs/zh/real_data_validation_datasets.md ABI SCAPP node on SRR11038083 legacy-sha256:789f08d8664e214a29d7bd62b97873458877b42d46c691816e3e1d9157e4a482 downloads/abi_scapp/tables/plasmid_predictions.tsv 56eaea090d98390bbecc5153891865b36b2d12b59f6ad844ce8c149b198644ee downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 ABI SCAPP node abi_scapp_precision 0.1262135922330097 13 103 fraction 1 /docs/zh/real_data_validation_datasets.md Against paper-method gold standard from PLSDB 2018-12-05; not paper-exact legacy-sha256:789f08d8664e214a29d7bd62b97873458877b42d46c691816e3e1d9157e4a482 downloads/abi_scapp/tables/plasmid_predictions.tsv 56eaea090d98390bbecc5153891865b36b2d12b59f6ad844ce8c149b198644ee downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 ABI SCAPP node abi_scapp_recall 0.8160919540229885 71 87 fraction 1 /docs/zh/real_data_validation_datasets.md Against paper-method gold standard from PLSDB 2018-12-05; not paper-exact legacy-sha256:789f08d8664e214a29d7bd62b97873458877b42d46c691816e3e1d9157e4a482 downloads/abi_scapp/tables/plasmid_predictions.tsv 56eaea090d98390bbecc5153891865b36b2d12b59f6ad844ce8c149b198644ee downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0 biological_validation flagship_case_study claim_eligible metagenomic_plasmid SRR11038083 ABI SCAPP node abi_scapp_f1 0.21861676930364757 fraction 1 /docs/zh/real_data_validation_datasets.md Harmonic mean of precision 13/103 and recall 71/87 legacy-sha256:789f08d8664e214a29d7bd62b97873458877b42d46c691816e3e1d9157e4a482 downloads/abi_scapp/tables/plasmid_predictions.tsv 56eaea090d98390bbecc5153891865b36b2d12b59f6ad844ce8c149b198644ee downloads/scapp_original/three_way_comparison.tsv 138cb6eaa0001712bb150eaea888452538efc858d29759051adc32a497af6fc0