{
  "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    "withdrawn": 88,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"
  }
}