{ "type": "genome", "identifier": "GCF_900156205.1", "organism": "Leptospira interrogans", "title": "Leptospira interrogans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900156205.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421689", "wgs_master": "FTNA00000000.1", "refseq_category": "na", "taxid": "173", "species_taxid": "173", "organism_name": "Leptospira interrogans", "infraspecific_name": "strain=ATCC 43642", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/15", "asm_name": "IMG-taxon 2681812812 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900156205.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/156/205/GCF_900156205.1_IMG-taxon_2681812812_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4594670", "genome_size_ungapped": "4589987", "gc_percent": "35.000000", "replicon_count": "0", "scaffold_count": "57", "contig_count": "57", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900156205.1-RS_2024_04_25", "annotation_date": "2024-04-25", "total_gene_count": "3782", "protein_coding_gene_count": "3611", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-15", "dateModified": "2017-01-15", "datePublished": "2017-01-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira interrogans" ], "sample_taxid": [ "173" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.280 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4594670", "Number of Sequences": "57", "Longest Sequences (bp)": "350340", "N50 (bp)": "133191", "Gap Ratio (%)": "0.101922", "GCcontent (%)": "35.0", "Number of CDSs": "3563", "Average Protein Length": "316.7", "Coding Ratio (%)": "73.7", "Number of rRNAs": "5", "Number of tRNAs": "37", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira interrogans", "strain": "strain=ATCC 43642", "accession": "GCA_900156205.1", "taxid": 173, "species_taxid": 173, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1503, "total_fragments": 1505, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira interrogans", "strain": "strain=RGA", "accession": "GCA_000343165.1", "taxid": 173, "species_taxid": 173, "relation_to_type": "type", "validated": true, "ani": 99.9129, "matched_fragments": 1430, "total_fragments": 1505, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira kirschneri", "strain": "strain=3522 CT", "accession": "GCA_000243695.3", "taxid": 29507, "species_taxid": 29507, "relation_to_type": "type", "validated": true, "ani": 90.6756, "matched_fragments": 1316, "total_fragments": 1505, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira noguchii", "strain": "strain=CZ214", "accession": "GCA_000306255.2", "taxid": 28182, "species_taxid": 28182, "relation_to_type": "suspected-type", "validated": true, "ani": 88.7276, "matched_fragments": 1290, "total_fragments": 1505, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira alstonii", "strain": "strain=79601", "accession": "GCA_000347175.1", "taxid": 28452, "species_taxid": 28452, "relation_to_type": "type", "validated": true, "ani": 80.2647, "matched_fragments": 896, "total_fragments": 1505, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira alexanderi", "strain": "strain=L 60", "accession": "GCA_000243815.3", "taxid": 100053, "species_taxid": 100053, "relation_to_type": "type", "validated": true, "ani": 80.0556, "matched_fragments": 853, "total_fragments": 1505, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira borgpetersenii", "strain": "strain=DSM 21538", "accession": "GCA_003046425.1", "taxid": 174, "species_taxid": 174, "relation_to_type": "type", "validated": true, "ani": 79.9209, "matched_fragments": 825, "total_fragments": 1505, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900156205.1", "gtdb_species": "s__Leptospira interrogans", "ani": 100.0, "matched_fragments": 1503, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.34", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 353, "status": "conclusive" }, { "accession": "GCF_000243695.2", "gtdb_species": "s__Leptospira kirschneri", "ani": 90.6546, "matched_fragments": 1319, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "97.03", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 36, "status": "-" }, { "accession": "GCF_000306255.2", "gtdb_species": "s__Leptospira noguchii", "ani": 88.7433, "matched_fragments": 1290, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.46", "min_intra_species_ani": "95.50", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.81", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_000347175.1", "gtdb_species": "s__Leptospira alstonii", "ani": 80.2504, "matched_fragments": 897, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000332415.1", "gtdb_species": "s__Leptospira weilii_A", "ani": 80.2376, "matched_fragments": 873, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "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_000243815.2", "gtdb_species": "s__Leptospira alexanderi", "ani": 80.0688, "matched_fragments": 849, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_000244815.1", "gtdb_species": "s__Leptospira weilii", "ani": 79.9199, "matched_fragments": 822, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.50", "min_intra_species_ani": "95.12", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_003046425.1", "gtdb_species": "s__Leptospira borgpetersenii", "ani": 79.9102, "matched_fragments": 827, "total_fragments": 1505, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "97.82", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 148, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.8, "cell_length": 0.954, "doubling_h": 1.009, "growth_tmp": 29.0, "optimum_tmp": 28.962, "optimum_ph": 7.4, "genome_size": 4673384.673, "gc_content": 34.972, "coding_genes": 3821.538, "rRNA16S_genes": 2.0, "tRNA_genes": 37.0, "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 }, "_genome_taxon": [ "Leptospira", "interrogans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }