{ "type": "genome", "identifier": "GCA_000205145.2", "organism": "Leptospirillum rubarum", "title": "Leptospirillum rubarum", "description": "derived from metagenome; incomplete metagenome", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_000205145.2", "bioproject": "PRJNA18537", "biosample": "SAMN02954271", "wgs_master": "AAWO00000000.1", "refseq_category": "na", "taxid": "419542", "species_taxid": "419542", "organism_name": "Leptospirillum rubarum", "infraspecific_name": "", "isolate": "", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2007/02/06", "asm_name": "ASM20514v2", "submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCF_000205145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/205/145/GCA_000205145.2_ASM20514v2", "excluded_from_refseq": "derived from metagenome; incomplete metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2007-02-06", "dateModified": "2007-02-06", "datePublished": "2007-02-06", "_annotation": { "sample_count": 1, "sample_organism": [ "mine drainage metagenome" ], "sample_taxid": [ "410659" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Ultra Back A (UBA) site of Richmond Mine (elevation 3100ft) at Iron Mountain, CA" ], "sample_host_location_id": [], "data_size": "0.734 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 97.68, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2636861", "Number of Sequences": "8", "Longest Sequences (bp)": "697839", "N50 (bp)": "405847", "Gap Ratio (%)": "0.150406", "GCcontent (%)": "54.7", "Number of CDSs": "2560", "Average Protein Length": "299.3", "Coding Ratio (%)": "87.2", "Number of rRNAs": "4", "Number of tRNAs": "48", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospirillum ferriphilum", "strain": "strain=DSM 14647", "accession": "GCA_000755505.1", "taxid": 178606, "species_taxid": 178606, "relation_to_type": "suspected-type", "validated": true, "ani": 92.3972, "matched_fragments": 682, "total_fragments": 875, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 97.68, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000299235.1", "gtdb_species": "s__Leptospirillum_A rubarum", "ani": 97.4544, "matched_fragments": 699, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota_A;c__Leptospirillia;o__Leptospirillales;f__Leptospirillaceae;g__Leptospirillum_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.14", "min_intra_species_ani": "96.51", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.83", "num_clustered_genomes": 20, "status": "conclusive" }, { "accession": "GCF_000755505.1", "gtdb_species": "s__Leptospirillum_A ferriphilum", "ani": 92.3972, "matched_fragments": 682, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota_A;c__Leptospirillia;o__Leptospirillales;f__Leptospirillaceae;g__Leptospirillum_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_011332985.1", "gtdb_species": "s__Leptospirillum_A ferriphilum_B", "ani": 78.0563, "matched_fragments": 209, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota_A;c__Leptospirillia;o__Leptospirillales;f__Leptospirillaceae;g__Leptospirillum_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000284315.1", "gtdb_species": "s__Leptospirillum ferrooxidans", "ani": 77.2995, "matched_fragments": 71, "total_fragments": 875, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota_A;c__Leptospirillia;o__Leptospirillales;f__Leptospirillaceae;g__Leptospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.046, "cell_length": null, "doubling_h": 0.776, "growth_tmp": 36.1, "optimum_tmp": 37.75, "optimum_ph": 1.65, "genome_size": 2474099.361, "gc_content": 52.2, "coding_genes": 2404.133, "rRNA16S_genes": 2.5, "tRNA_genes": 49.666, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Nitrospirota_A", "c__Leptospirillia", "o__Leptospirillales", "f__Leptospirillaceae", "g__Leptospirillum_A", "s__Leptospirillum_A rubarum" ], "_genome_taxon": [ "Leptospirillum", "rubarum", "d__Bacteria", "p__Nitrospirota_A", "c__Leptospirillia", "o__Leptospirillales", "f__Leptospirillaceae", "g__Leptospirillum_A", "s__Leptospirillum_A rubarum", "Bacteria", "Nitrospirota", "A", "Leptospirillia", "Leptospirillales", "Leptospirillaceae", "Leptospirillum", "A", "Leptospirillum", "A", "rubarum" ], "_meo": [ { "id": "MEO_0000034", "label": "acid mine drainage" } ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }