{ "type": "genome", "identifier": "GCF_003114835.2", "organism": "Leptospira kobayashii", "title": "Leptospira kobayashii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Laboratory of Parasitology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003114835.2", "bioproject": "PRJNA224116", "biosample": "SAMD00111976", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1917830", "species_taxid": "1917830", "organism_name": "Leptospira kobayashii", "infraspecific_name": "strain=E30", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/09/09", "asm_name": "ASM311483v3", "asm_submitter": "Laboratory of Parasitology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University", "gbrs_paired_asm": "GCA_003114835.3", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/114/835/GCF_003114835.2_ASM311483v3", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4304943", "genome_size_ungapped": "4304943", "gc_percent": "40.500000", "replicon_count": "3", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003114835.2-RS_2024_04_12", "annotation_date": "2024-04-12", "total_gene_count": "3948", "protein_coding_gene_count": "3885", "non_coding_gene_count": "43", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-09-09", "dateModified": "2021-09-09", "datePublished": "2021-09-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira kobayashii" ], "sample_taxid": [ "1917830" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Gifu, Mizunami" ], "sample_host_location_id": [], "data_size": "1.209 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)": "4304943", "Number of Sequences": "3", "Longest Sequences (bp)": "3985339", "N50 (bp)": "3985339", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.7", "Number of CDSs": "3901", "Average Protein Length": "338.0", "Coding Ratio (%)": "91.9", "Number of rRNAs": "6", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira kobayashii", "strain": "strain=E30", "accession": "GCA_003114835.3", "taxid": 1917830, "species_taxid": 1917830, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1434, "total_fragments": 1434, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira ilyithenensis", "strain": "strain=201400974", "accession": "GCA_004771005.1", "taxid": 2484901, "species_taxid": 2484901, "relation_to_type": "type", "validated": true, "ani": 88.0348, "matched_fragments": 1209, "total_fragments": 1434, "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": 77.5225, "matched_fragments": 242, "total_fragments": 1434, "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": 77.452, "matched_fragments": 241, "total_fragments": 1434, "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": 77.3852, "matched_fragments": 212, "total_fragments": 1434, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira ognonensis", "strain": "strain=201702476", "accession": "GCA_004770745.1", "taxid": 2484945, "species_taxid": 2484945, "relation_to_type": "type", "validated": true, "ani": 77.3735, "matched_fragments": 205, "total_fragments": 1434, "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": 77.33, "matched_fragments": 220, "total_fragments": 1434, "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": 77.3147, "matched_fragments": 237, "total_fragments": 1434, "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": 77.3024, "matched_fragments": 247, "total_fragments": 1434, "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": 77.2472, "matched_fragments": 234, "total_fragments": 1434, "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": 77.2269, "matched_fragments": 242, "total_fragments": 1434, "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": 77.1592, "matched_fragments": 227, "total_fragments": 1434, "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": 77.1269, "matched_fragments": 223, "total_fragments": 1434, "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": 76.3099, "matched_fragments": 55, "total_fragments": 1434, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003114835.1", "gtdb_species": "s__Leptospira_A kobayashii", "ani": 99.9848, "matched_fragments": 1417, "total_fragments": 1434, "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": "conclusive" }, { "accession": "GCF_004771005.1", "gtdb_species": "s__Leptospira_A ilyithenensis", "ani": 88.032, "matched_fragments": 1210, "total_fragments": 1434, "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_004770995.1", "gtdb_species": "s__Leptospira_A idonii", "ani": 78.4756, "matched_fragments": 516, "total_fragments": 1434, "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_004769575.1", "gtdb_species": "s__Leptospira_A perdikensis", "ani": 77.4946, "matched_fragments": 242, "total_fragments": 1434, 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0.0, "spiral_cell_shape": 0.9 }, "_genome_taxon": [ "Leptospira", "kobayashii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }