{ "type": "genome", "identifier": "GCF_004771275.1", "organism": "Leptospira fluminis", "title": "Leptospira fluminis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "INRS-Institut Armand-Frappier", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004771275.1", "bioproject": "PRJNA224116", "biosample": "SAMN10316443", "wgs_master": "RQEV00000000.1", "refseq_category": "reference genome", "taxid": "2484979", "species_taxid": "2484979", "organism_name": "Leptospira fluminis", "infraspecific_name": "strain=SCS5", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/10", "asm_name": "ASM477127v1", "asm_submitter": "INRS-Institut Armand-Frappier", "gbrs_paired_asm": "GCA_004771275.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/771/275/GCF_004771275.1_ASM477127v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3746420", "genome_size_ungapped": "3746420", "gc_percent": "47.500000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004771275.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "3439", "protein_coding_gene_count": "3379", "non_coding_gene_count": "44", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-10", "dateModified": "2019-04-10", "datePublished": "2019-04-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira fluminis" ], "sample_taxid": [ "2484979" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Malaysia" ], "sample_host_location_id": [], "data_size": "1.060 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)": "3746420", "Number of Sequences": "18", "Longest Sequences (bp)": "718176", "N50 (bp)": "325090", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.7", "Number of CDSs": "3391", "Average Protein Length": "336.4", "Coding Ratio (%)": "91.3", "Number of rRNAs": "4", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira fluminis", "strain": "strain=SCS5", "accession": "GCA_004771275.1", "taxid": 2484979, "species_taxid": 2484979, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1240, "total_fragments": 1240, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira fletcheri", "strain": "strain=SSW15", "accession": "GCA_004769195.1", "taxid": 2484981, "species_taxid": 2484981, "relation_to_type": "type", "validated": true, "ani": 91.1102, "matched_fragments": 1153, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira inadai", "strain": "strain=10", "accession": "GCA_000243675.3", "taxid": 29506, "species_taxid": 29506, "relation_to_type": "type", "validated": true, "ani": 78.4502, "matched_fragments": 478, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira fainei", "strain": "strain=BUT 6", "accession": "GCA_000306235.2", "taxid": 48782, "species_taxid": 48782, "relation_to_type": "type", "validated": true, "ani": 78.4355, "matched_fragments": 438, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira broomii", "strain": "strain=5399", "accession": "GCA_000243715.3", "taxid": 301541, "species_taxid": 301541, "relation_to_type": "type", "validated": true, "ani": 78.3295, "matched_fragments": 445, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira wolffii", "strain": "strain=Khorat-H2", "accession": "GCA_000306115.2", "taxid": 409998, "species_taxid": 409998, "relation_to_type": "type", "validated": true, "ani": 77.5086, "matched_fragments": 320, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira johnsonii", "strain": "strain=E8", "accession": "GCA_003112675.1", "taxid": 1917820, "species_taxid": 1917820, "relation_to_type": "type", "validated": true, "ani": 77.1933, "matched_fragments": 231, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira hartskeerlii", "strain": "strain=MCA2-B-A3", "accession": "GCA_002811475.1", "taxid": 2023177, "species_taxid": 2023177, "relation_to_type": "type", "validated": true, "ani": 76.9255, "matched_fragments": 230, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira ainlahdjerensis", "strain": "strain=201903070", "accession": "GCA_016919175.1", "taxid": 2810033, "species_taxid": 2810033, "relation_to_type": "type", "validated": true, "ani": 75.9749, "matched_fragments": 119, "total_fragments": 1240, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004771275.1", "gtdb_species": "s__Leptospira_B fluminis", "ani": 100.0, "matched_fragments": 1240, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "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": "conclusive" }, { "accession": "GCF_004769195.1", "gtdb_species": "s__Leptospira_B fletcheri", "ani": 91.1227, "matched_fragments": 1152, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "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_000243675.2", "gtdb_species": "s__Leptospira_B inadai", "ani": 78.4537, "matched_fragments": 477, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000306235.2", "gtdb_species": "s__Leptospira_B fainei", "ani": 78.4355, "matched_fragments": 438, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "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_000243715.2", "gtdb_species": "s__Leptospira_B broomii", "ani": 78.3295, "matched_fragments": 445, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "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_000306115.2", "gtdb_species": "s__Leptospira_B wolffii", "ani": 77.5127, "matched_fragments": 321, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.66", "min_intra_species_ani": "96.35", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003112675.1", "gtdb_species": "s__Leptospira_B johnsonii", "ani": 77.1864, "matched_fragments": 230, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "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_002811475.1", "gtdb_species": "s__Leptospira_B hartskeerlii", "ani": 76.9255, "matched_fragments": 230, "total_fragments": 1240, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "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": "GCF_000244815.1", "gtdb_species": "s__Leptospira weilii", "ani": 76.2034, "matched_fragments": 86, "total_fragments": 1240, "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": "-" } ] }, "_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", "fluminis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }