| { |
| "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" |
| } |
| } |
|
|
