{ "type": "genome", "identifier": "GCF_002812085.1", "organism": "Leptospira levettii", "title": "Leptospira levettii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institut Pasteur Montevideo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002812085.1", "bioproject": "PRJNA224116", "biosample": "SAMN07411430", "wgs_master": "NPDM00000000.1", "refseq_category": "reference genome", "taxid": "2023178", "species_taxid": "2023178", "organism_name": "Leptospira levettii", "infraspecific_name": "strain=MCA2-B-A1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/12/05", "asm_name": "ASM281208v1", "asm_submitter": "Institut Pasteur Montevideo", "gbrs_paired_asm": "GCA_002812085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/812/085/GCF_002812085.1_ASM281208v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3875926", "genome_size_ungapped": "3875916", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "14", "contig_count": "14", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002812085.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "3620", "protein_coding_gene_count": "3560", "non_coding_gene_count": "44", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-12-05", "dateModified": "2017-12-05", "datePublished": "2017-12-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira levettii" ], "sample_taxid": [ "2023178" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "New Caledonia" ], "sample_host_location_id": [], "data_size": "1.088 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)": "3875926", "Number of Sequences": "14", "Longest Sequences (bp)": "1625029", "N50 (bp)": "772998", "Gap Ratio (%)": "0.000258", "GCcontent (%)": "37.6", "Number of CDSs": "3591", "Average Protein Length": "335.4", "Coding Ratio (%)": "93.2", "Number of rRNAs": "2", "Number of tRNAs": "35", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1284, "total_fragments": 1285, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira ellinghausenii", "strain": "strain=E18", "accession": "GCA_003114815.1", "taxid": 1917822, "species_taxid": 1917822, "relation_to_type": "type", "validated": true, "ani": 91.95, "matched_fragments": 1186, "total_fragments": 1285, "ani_threshold": 95, "status": "below_threshold" }, { "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": 83.4531, "matched_fragments": 967, "total_fragments": 1285, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira yanagawae", "strain": "strain=Sao Paulo", "accession": "GCA_000332475.2", "taxid": 293069, "species_taxid": 293069, "relation_to_type": "type", "validated": true, "ani": 83.2224, "matched_fragments": 951, "total_fragments": 1285, "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": 81.1792, "matched_fragments": 765, "total_fragments": 1285, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira vanthielii", "strain": "strain=Waz Holland", "accession": "GCA_000332455.2", "taxid": 293085, "species_taxid": 293085, "relation_to_type": "type", "validated": true, "ani": 80.9708, "matched_fragments": 741, "total_fragments": 1285, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira brenneri", "strain": "strain=JW2-C-A2", "accession": "GCA_002812125.1", "taxid": 2023182, "species_taxid": 2023182, "relation_to_type": "type", "validated": true, "ani": 80.9467, "matched_fragments": 737, "total_fragments": 1285, "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": 80.8963, "matched_fragments": 753, "total_fragments": 1285, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002812085.1", "gtdb_species": "s__Leptospira_A levettii", "ani": 100.0, "matched_fragments": 1284, "total_fragments": 1285, "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", "min_intra_species_af": "0.91", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCF_003114815.1", "gtdb_species": "s__Leptospira_A ellinghausenii", "ani": 91.95, "matched_fragments": 1186, "total_fragments": 1285, "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": "GCA_016742255.1", "gtdb_species": "s__Leptospira_A sp016742255", "ani": 91.9183, "matched_fragments": 1130, "total_fragments": 1285, "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_004769665.1", "gtdb_species": "s__Leptospira_A kemamanensis", "ani": 84.5527, "matched_fragments": 974, "total_fragments": 1285, "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_004769525.1", "gtdb_species": "s__Leptospira_A bouyouniensis", "ani": 83.4922, "matched_fragments": 997, "total_fragments": 1285, "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_000017685.1", "gtdb_species": "s__Leptospira_A biflexa", "ani": 83.4483, "matched_fragments": 967, "total_fragments": 1285, "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_004769635.1", "gtdb_species": "s__Leptospira_A jelokensis", "ani": 83.3417, "matched_fragments": 938, "total_fragments": 1285, "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_000332475.2", "gtdb_species": "s__Leptospira_A yanagawae", "ani": 83.2408, "matched_fragments": 949, "total_fragments": 1285, "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": "-" } ] }, "_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", "levettii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }