| { |
| "1_nfix_rebuild": { |
| "wp3_invalid_negative": 41, |
| "wp3_invalid_verdicts": 41, |
| "wp3_verdicts_unmatched": 0, |
| "misread_cn_ratio_cell": 481, |
| "gene_count_misread_as_phenotype": 18, |
| "hand_read_rows": 6, |
| "usable_rows_without_species_taxid": 4082, |
| "not_a_single_microbial_species": 208, |
| "species_v01_usable": 551, |
| "species_v02_usable": 475, |
| "v02_fixers": 440, |
| "v02_nonfixers": 35, |
| "added": 12, |
| "withdrawn": 88, |
| "flipped": 0, |
| "restored_from_conflicted": 12 |
| }, |
| "9_evidence_tiers": { |
| "n_free_growth_without_verified_control": 10 |
| }, |
| "licence": { |
| "nfixdb_genotype_rows_left_out": 2471 |
| }, |
| "11_duplicates": { |
| "genome_rows_v01": 14966, |
| "duplicate_accession_rows_removed": 449, |
| "strains_with_several_genomes": 0, |
| "genome_rows_v02": 14517, |
| "representative_rule": "CheckM2 (else NCBI CheckM) completeness, contamination, contigs, N50" |
| }, |
| "2_targets": { |
| "genomes_with_protein_fasta": 14429, |
| "nitrogenase_carrier_true": 1063, |
| "nitrogenase_carrier_false": 13366, |
| "nitrogenase_unknown": 88, |
| "methods_disagree": 25, |
| "method": "NCBIfam nitrogen-fixation HMMs at trusted cutoffs (nifH plus nifD+K, vnfD+K or anfD+K); PGAP product names (scripts/poc_set/nif.py) as a second call; the HMM call wins where both exist" |
| }, |
| "7_taxonomy": { |
| "genomes_in_gtdb": 14039, |
| "genomes_not_in_gtdb": 478, |
| "gtdb_species_clusters": 13175, |
| "gtdb_release": "v232", |
| "synonyms": "NCBI names.dmp synonyms only; LPSN not added (needs an LPSN account)" |
| }, |
| "3_veto": { |
| "genomes_with_species_label": 322, |
| "fixer_label_vetoed_no_nitrogenase": 157, |
| "nonfixer_label_on_carrier_kept_flagged": 0, |
| "nitrogenase_unknown": 2, |
| "phenotype_label_1": 143, |
| "phenotype_label_0": 22 |
| }, |
| "4_strain_tier": { |
| "nfix_genomes_strain_tier": 25, |
| "nfix_genomes_species_tier": 297, |
| "strain_tier_disagrees_with_species": 0, |
| "strain_trait_rows": 126085, |
| "strains": 29754, |
| "strains_with_own_genome": 11869 |
| }, |
| "5_conflicts": { |
| "strains_conflicting_gram": 29, |
| "strains_conflicting_motility": 79, |
| "strains_conflicting_spore": 5, |
| "strains_conflicting_oxygen": 1196, |
| "strains_conflicting_shape": 208, |
| "species_consensus_coverage": { |
| "gram": { |
| "species_with_value_v01": 11709, |
| "species_with_value_v02": 11709, |
| "v02_values_flagged_may_include_predicted": 2009 |
| }, |
| "shape": { |
| "species_with_value_v01": 9459, |
| "species_with_value_v02": 9459, |
| "v02_values_flagged_may_include_predicted": 1638 |
| }, |
| "motility": { |
| "species_with_value_v01": 9509, |
| "species_with_value_v02": 9509, |
| "v02_values_flagged_may_include_predicted": 1609 |
| }, |
| "spore": { |
| "species_with_value_v01": 6869, |
| "species_with_value_v02": 6869, |
| "v02_values_flagged_may_include_predicted": 2024 |
| }, |
| "oxygen": { |
| "species_with_value_v01": 9818, |
| "species_with_value_v02": 9818, |
| "v02_values_flagged_may_include_predicted": 0 |
| } |
| }, |
| "rule": "strict consensus unchanged (all sources agree); <trait>_modal and <trait>_agreement added; values whose Madin sources include ProTraits count and are flagged <trait>_may_include_predicted; FAPROTAX rows do not count" |
| }, |
| "6_vocabulary": { |
| "unmapped_values_set_other": 74, |
| "mapping": { |
| "gram": { |
| "positive": "positive", |
| "negative": "negative", |
| "variable": "variable" |
| }, |
| "motility": { |
| "yes": "motile", |
| "no": "nonmotile" |
| }, |
| "spore": { |
| "yes": "yes", |
| "no": "no" |
| }, |
| "oxygen": { |
| "aerobe": "aerobic", |
| "obligate aerobe": "aerobic", |
| "anaerobe": "anaerobic", |
| "obligate anaerobe": "anaerobic", |
| "facultative anaerobe": "facultative", |
| "facultative aerobe": "facultative", |
| "microaerophile": "microaerophilic", |
| "aerotolerant": "anaerobic", |
| "microaerotolerant": "microaerophilic" |
| }, |
| "shape": { |
| "rod-shaped": "rod", |
| "coccus-shaped": "coccus", |
| "sphere-shaped": "coccus", |
| "diplococcus-shaped": "coccus", |
| "oval-shaped": "coccobacillus", |
| "ovoid-shaped": "coccobacillus", |
| "ellipsoidal": "coccobacillus", |
| "filament-shaped": "filament", |
| "curved-shaped": "vibrio", |
| "vibrio-shaped": "vibrio", |
| "crescent-shaped": "vibrio", |
| "spiral-shaped": "spiral", |
| "helical-shaped": "spiral", |
| "pleomorphic-shaped": "pleomorphic" |
| } |
| }, |
| "bacdive_cultivation_temperature_rows_relabelled": 10062, |
| "bacdive_optimum_species_added": 3267 |
| }, |
| "8_provenance": { |
| "curated": 133043, |
| "curated_may_include_predicted": 10818, |
| "culture_condition": 10062, |
| "text_mined": 6020, |
| "predicted": 4826 |
| }, |
| "10_growth_rates": { |
| "rows": 1004, |
| "flagged_implausible": 1, |
| "unit": "specific growth rate per hour; doubling_time_h = ln 2 / mu", |
| "conditions": "medium and temperature are not recorded by Madin or the \u00b5GrowthDB summary; v0.1's 'standard medium' was an assumption and is now marked as one", |
| "quarantined_umol_nitrogenase_rates": "not in the package (no nitrogenase-rate table yet)" |
| }, |
| "12_label_noise": { |
| "sample_rows": 677, |
| "status": "drawn; hand adjudication pending", |
| "file": "data/qc/v0.2_label_audit_sample.csv" |
| } |
| } |
