{ "type": "genome", "identifier": "GCF_000017685.1", "organism": "Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'", "title": "Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institut Pasteur", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000017685.1", "bioproject": "PRJNA224116", "biosample": "SAMN02603347", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "456481", "species_taxid": "172", "organism_name": "Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'", "infraspecific_name": "strain=Patoc 1 (Paris)", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2008/02/13", "asm_name": "ASM1768v1", "asm_submitter": "Institut Pasteur", "gbrs_paired_asm": "GCA_000017685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/017/685/GCF_000017685.1_ASM1768v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3951448", "genome_size_ungapped": "3951448", "gc_percent": "39.000000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000017685.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3717", "protein_coding_gene_count": "3651", "non_coding_gene_count": "43", "pubmed_id": "18270594" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2008-02-13", "dateModified": "2008-02-13", "datePublished": "2008-02-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)'" ], "sample_taxid": [ "456481" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.108 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)": "3951448", "Number of Sequences": "3", "Longest Sequences (bp)": "3599677", "N50 (bp)": "3599677", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.9", "Number of CDSs": "3691", "Average Protein Length": "328.4", "Coding Ratio (%)": "92.0", "Number of rRNAs": "6", "Number of tRNAs": "35", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1313, "total_fragments": 1315, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira yanagawae", "strain": "strain=Sao Paulo", "accession": "GCA_000332475.2", "taxid": 293069, "species_taxid": 293069, "relation_to_type": "type", "validated": true, "ani": 83.9937, "matched_fragments": 980, "total_fragments": 1315, "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": 83.4254, "matched_fragments": 992, "total_fragments": 1315, "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": 83.3936, "matched_fragments": 978, "total_fragments": 1315, "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": 81.1476, "matched_fragments": 762, "total_fragments": 1315, "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": 81.0931, "matched_fragments": 802, "total_fragments": 1315, "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": 81.0134, "matched_fragments": 776, "total_fragments": 1315, "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": 80.8556, "matched_fragments": 799, "total_fragments": 1315, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira ryugenii", "strain": "strain=YH101", "accession": "GCA_003114855.1", "taxid": 1917863, "species_taxid": 1917863, "relation_to_type": "type", "validated": true, "ani": 76.9083, "matched_fragments": 179, "total_fragments": 1315, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000017685.1", "gtdb_species": "s__Leptospira_A biflexa", "ani": 100.0, "matched_fragments": 1313, "total_fragments": 1315, "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": "conclusive" }, { "accession": "GCF_004769525.1", "gtdb_species": "s__Leptospira_A bouyouniensis", "ani": 84.4517, "matched_fragments": 1079, "total_fragments": 1315, "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_000332475.2", "gtdb_species": "s__Leptospira_A yanagawae", "ani": 83.9975, "matched_fragments": 980, "total_fragments": 1315, "gtdb_taxonomy": 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38.422, "coding_genes": 3680.4, "rRNA16S_genes": 2.0, "tRNA_genes": 35.0, "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", "biflexa", "serovar", "Patoc", "strain", "'Patoc", "1", "(Paris)'" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }