{
  "configs": {
    "enterococcus_clean_v2_host_assemblies": {
      "columns": [
        "assembly_accession",
        "sequence_db_assembly_accession",
        "sequence_db_source",
        "primary_evidence_assembly_accession",
        "evidence_assembly_accessions",
        "evidence_sources",
        "manifest_match_types",
        "n_evidence_assembly_accessions",
        "taxid",
        "organism_name",
        "source_db",
        "assembly_level",
        "target_group",
        "enterococcus_match_evidence",
        "n_representative_plasmids",
        "n_member_plasmids",
        "n_link_rows",
        "chunk_id",
        "chunk_path",
        "n_rows",
        "n_plasmid_rows",
        "n_non_plasmid_rows",
        "n_bp",
        "in_sequence_db",
        "genus_taxid",
        "host_taxa_id",
        "non_plasmid_contigs",
        "non_plasmid_bp",
        "has_non_plasmid_contigs"
      ],
      "contains_sequence_column": false,
      "rows": 1497
    },
    "enterococcus_clean_v2_host_contigs": {
      "columns": [
        "assembly_accession",
        "sequence_id",
        "new_contig_id",
        "original_contig_id",
        "source_contig_id",
        "sampler_contig_id",
        "seq_length",
        "chunk_path"
      ],
      "contains_sequence_column": false,
      "rows": 4530
    },
    "enterococcus_clean_v2_plasmid_to_assembly_links": {
      "columns": [
        "cluster_id",
        "representative_plasmid_id",
        "member_plasmid_id",
        "member_is_representative",
        "assembly_accession",
        "plasmid_accession",
        "assembly_source",
        "source_db",
        "organism_name",
        "taxid",
        "target_group",
        "assembly_level",
        "seq_length",
        "chr_name",
        "sequence_name",
        "refseq_seq_accession",
        "genbank_seq_accession",
        "accession_class",
        "molecule_type",
        "plasmid_evidence_fields",
        "plasmid_evidence_terms",
        "ftp_path",
        "assembly_unit",
        "role",
        "gc_percent",
        "ucsc_style_name",
        "unlocalized_count",
        "assembly_unplaced_count",
        "source_batch_id",
        "source_requested_accession",
        "source_raw_file",
        "plasmid_confidence",
        "plasmid_heuristic_version",
        "has_refseq",
        "has_genbank",
        "assembly_source_priority",
        "_source_link_row",
        "paired_assembly_accession",
        "assembly_pair_key",
        "refseq_assembly_accession",
        "genbank_assembly_accession",
        "enterococcus_genus_taxid",
        "enterococcus_match_evidence",
        "sequence_db_assembly_accession",
        "manifest_match_type",
        "requested_source",
        "sequence_db_source"
      ],
      "contains_sequence_column": false,
      "rows": 7916
    },
    "enterococcus_clean_v2_plasmids": {
      "columns": [
        "plasmid_id",
        "seq_length",
        "fasta_id",
        "cluster_id",
        "cluster_size",
        "sequence_md5",
        "n_member_assemblies",
        "n_unique_assemblies",
        "n_member_assembly_link_rows",
        "filename",
        "orientation",
        "topology",
        "labels",
        "raw_label",
        "genus_taxid",
        "host_genus_taxid",
        "sequence_id",
        "plasmid_accession",
        "refseq_seq_accession",
        "genbank_seq_accession",
        "organism_name",
        "taxid",
        "source_db",
        "assembly_accession",
        "refseq_assembly_accession",
        "genbank_assembly_accession",
        "filter_reasons",
        "has_high_quality_chromosome_hit",
        "n_hq_chromosome_contigs",
        "n_hq_chromosome_assemblies",
        "n_near_complete_chromosome_contigs",
        "n_near_complete_chromosome_assemblies",
        "is_excluded"
      ],
      "contains_sequence_column": false,
      "rows": 2519
    },
    "enterococcus_clean_v2_segments": {
      "columns": [
        "segment_id",
        "sequence_id",
        "source_segment_id",
        "labels",
        "segment",
        "segment_length",
        "strand",
        "source_type",
        "source_id",
        "plasmid_id",
        "assembly_accession",
        "sequence_db_assembly_accession",
        "evidence_assembly_accessions",
        "original_contig_id",
        "new_contig_id",
        "segment_start",
        "segment_end",
        "source_seq_length",
        "seq_length",
        "genus_taxid",
        "host_genus_taxid",
        "raw_label",
        "orientation",
        "filtered_by_plasmid",
        "best_plasmid_id",
        "best_plasmid_qcov",
        "best_plasmid_pid",
        "best_plasmid_cov_bp",
        "best_plasmid_aln_bp",
        "best_plasmid_length",
        "host_minimap_aligned",
        "n_paf_records",
        "best_plasmid_id_ignore_top10",
        "best_plasmid_qcov_ignore_top10",
        "best_plasmid_pid_ignore_top10",
        "best_plasmid_cov_bp_ignore_top10",
        "best_plasmid_aln_bp_ignore_top10",
        "filtered_by_plasmid_ignore_top10",
        "recoverable_if_ignore_top10",
        "still_filtered_if_ignore_top10",
        "newly_filtered_if_ignore_top10",
        "host_segment_id",
        "host_candidate_id",
        "training_eligible_current_clean",
        "is_problematic_segment",
        "problematic_reasons",
        "problematic_side"
      ],
      "contains_sequence_column": true,
      "rows": 910900
    }
  },
  "created_at": "2026-07-09T11:43:33.321339+00:00",
  "filter_semantics": {
    "all_rows": "load the enterococcus_clean_v2_segments config without filtering",
    "current_clean_training": "training_eligible_current_clean == True",
    "flagged_host_segments": "source_type == 'host' and filtered_by_plasmid == True"
  },
  "primary_key": {
    "column": "segment_id",
    "config": "enterococcus_clean_v2_segments",
    "type": "int64"
  },
  "source_sequence_key": {
    "column": "sequence_id",
    "config": "enterococcus_clean_v2_segments",
    "semantics": "contiguous source-sequence grouping ID",
    "type": "int64"
  }
}