{ "type": "genome", "identifier": "GCF_000332475.2", "organism": "Leptospira yanagawae serovar Saopaulo str. Sao Paulo = ATCC 700523", "title": "Leptospira yanagawae serovar Saopaulo str. Sao Paulo = ATCC 700523", "description": "na", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000332475.2", "bioproject": "PRJNA224116", "biosample": "SAMN02436394", "wgs_master": "AOGX00000000.2", "refseq_category": "na", "taxid": "1249483", "species_taxid": "293069", "organism_name": "Leptospira yanagawae serovar Saopaulo str. Sao Paulo = ATCC 700523", "infraspecific_name": "strain=Sao Paulo", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/05/17", "asm_name": "gls454202v02", "asm_submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "GCA_000332475.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/332/475/GCF_000332475.2_gls454202v02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4056240", "genome_size_ungapped": "4056240", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "47", "contig_count": "47", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000332475.2-RS_2024_04_21", "annotation_date": "2024-04-21", "total_gene_count": "3858", "protein_coding_gene_count": "3782", "non_coding_gene_count": "44", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-05-17", "dateModified": "2013-05-17", "datePublished": "2013-05-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira yanagawae serovar Saopaulo str. Sao Paulo = ATCC 700523" ], "sample_taxid": [ "1249483" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil" ], "sample_host_location_id": [], "data_size": "1.140 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4056240", "Number of Sequences": "47", "Longest Sequences (bp)": "1322194", "N50 (bp)": "330086", "Gap Ratio (%)": "0.000025", "GCcontent (%)": "38.2", "Number of CDSs": "3811", "Average Protein Length": "322.3", "Coding Ratio (%)": "90.8", "Number of rRNAs": "6", "Number of tRNAs": "35", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira yanagawae", "strain": "strain=Sao Paulo", "accession": "GCA_000332475.2", "taxid": 293069, "species_taxid": 293069, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1329, "total_fragments": 1329, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira biflexa", "strain": "strain=Patoc 1 (Paris)", "accession": "GCA_000017685.1", "taxid": 172, "species_taxid": 172, "relation_to_type": "type", "validated": true, "ani": 83.9353, "matched_fragments": 996, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira levettii", "strain": "strain=MCA2-B-A1", "accession": "GCA_002812085.1", "taxid": 2023178, "species_taxid": 2023178, "relation_to_type": "type", "validated": true, "ani": 83.1883, "matched_fragments": 931, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira ellinghausenii", "strain": "strain=E18", "accession": "GCA_003114815.1", "taxid": 1917822, "species_taxid": 1917822, "relation_to_type": "type", "validated": true, "ani": 83.1364, "matched_fragments": 936, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira wolbachii", "strain": "strain=CDC", "accession": "GCA_000332515.2", "taxid": 29511, "species_taxid": 29511, "relation_to_type": "type", "validated": true, "ani": 81.1532, "matched_fragments": 729, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira abararensis", "strain": "strain=201903074", "accession": "GCA_016918735.1", "taxid": 2810036, "species_taxid": 2810036, "relation_to_type": "type", "validated": true, "ani": 81.0969, "matched_fragments": 733, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira meyeri", "strain": "strain=DSM 21537", "accession": "GCA_004368965.1", "taxid": 29508, "species_taxid": 29508, "relation_to_type": "type", "validated": true, "ani": 80.9872, "matched_fragments": 766, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira terpstrae", "strain": "strain=LT 11-33", "accession": "GCA_000332495.2", "taxid": 293075, "species_taxid": 293075, "relation_to_type": "type", "validated": true, "ani": 80.971, "matched_fragments": 759, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira harrisiae", "strain": "strain=FH2-B-A1", "accession": "GCA_002811945.1", "taxid": 2023189, "species_taxid": 2023189, "relation_to_type": "type", "validated": true, "ani": 80.9389, "matched_fragments": 751, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira chreensis", "strain": "strain=201903075", "accession": "GCA_016919165.1", "taxid": 2810035, "species_taxid": 2810035, "relation_to_type": "type", "validated": true, "ani": 80.935, "matched_fragments": 773, "total_fragments": 1329, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000332475.2", "gtdb_species": "s__Leptospira_A yanagawae", "ani": 100.0, "matched_fragments": 1329, "total_fragments": 1329, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_004769635.1", "gtdb_species": "s__Leptospira_A jelokensis", "ani": 89.2807, "matched_fragments": 1168, "total_fragments": 1329, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.57", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004769525.1", "gtdb_species": "s__Leptospira_A bouyouniensis", "ani": 85.4692, "matched_fragments": 999, "total_fragments": 1329, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.10", "min_intra_species_ani": "99.07", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004769665.1", "gtdb_species": "s__Leptospira_A kemamanensis", "ani": 84.3677, "matched_fragments": 1043, "total_fragments": 1329, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_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_000017685.1", "gtdb_species": "s__Leptospira_A biflexa", "ani": 83.9417, "matched_fragments": 994, "total_fragments": 1329, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "98.34", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002812085.1", "gtdb_species": "s__Leptospira_A levettii", "ani": 83.1788, "matched_fragments": 932, "total_fragments": 1329, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.25", "mean_intra_species_af": "0.94", 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"num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_004770145.1", "gtdb_species": "s__Leptospira_A bourretii", "ani": 81.0645, "matched_fragments": 784, "total_fragments": 1329, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "99.11", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.8, "cell_length": 0.954, "doubling_h": 1.009, "growth_tmp": 29.846, "optimum_tmp": 30.329, "optimum_ph": 7.4, "genome_size": 4295423.544, "gc_content": 39.557, "coding_genes": 3721.42, "rRNA16S_genes": 2.0, "tRNA_genes": 36.694, "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": 0.1, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.9 }, "_genome_taxon": [ "Leptospira", "yanagawae", "serovar", "Saopaulo", "str.", "Sao", "Paulo", "=", "ATCC", "700523" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }