{ "type": "genome", "identifier": "GCF_004368965.1", "organism": "Leptospira meyeri", "title": "Leptospira meyeri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004368965.1", "bioproject": "PRJNA224116", "biosample": "SAMN07621512", "wgs_master": "SORO00000000.1", "refseq_category": "reference genome", "taxid": "29508", "species_taxid": "29508", "organism_name": "Leptospira meyeri", "infraspecific_name": "strain=DSM 21537", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436896v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004368965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/368/965/GCF_004368965.1_ASM436896v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4237206", "genome_size_ungapped": "4237206", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "16", "contig_count": "16", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004368965.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3958", "protein_coding_gene_count": "3900", "non_coding_gene_count": "42", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira meyeri" ], "sample_taxid": [ "29508" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.191 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)": "4237206", "Number of Sequences": "16", "Longest Sequences (bp)": "3010043", "N50 (bp)": "3010043", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.0", "Number of CDSs": "3931", "Average Protein Length": "329.7", "Coding Ratio (%)": "91.8", "Number of rRNAs": "5", "Number of tRNAs": "35", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira meyeri", "strain": "strain=DSM 21537", "accession": "GCA_004368965.1", "taxid": 29508, "species_taxid": 29508, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1406, "total_fragments": 1406, "ani_threshold": 95, "status": "conclusive" }, { "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": 85.909, "matched_fragments": 1153, "total_fragments": 1406, "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": 83.4887, "matched_fragments": 1008, "total_fragments": 1406, "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": 83.4149, "matched_fragments": 1065, "total_fragments": 1406, "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": 83.3496, "matched_fragments": 1047, "total_fragments": 1406, "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": 83.316, "matched_fragments": 1048, "total_fragments": 1406, "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": 83.2334, "matched_fragments": 1051, "total_fragments": 1406, "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": 83.162, "matched_fragments": 1064, "total_fragments": 1406, "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": 81.0603, "matched_fragments": 763, "total_fragments": 1406, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004368965.1", "gtdb_species": "s__Leptospira_A meyeri", "ani": 100.0, "matched_fragments": 1406, "total_fragments": 1406, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.24", "min_intra_species_ani": "96.32", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCF_004770475.1", "gtdb_species": "s__Leptospira_A mtsangambouensis", "ani": 89.4479, "matched_fragments": 1244, "total_fragments": 1406, "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_004770145.1", "gtdb_species": "s__Leptospira_A bourretii", "ani": 89.317, "matched_fragments": 1247, "total_fragments": 1406, "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": "-" }, { "accession": "GCF_002811945.1", "gtdb_species": "s__Leptospira_A harrisiae", "ani": 85.8919, "matched_fragments": 1154, "total_fragments": 1406, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.94", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004770265.1", "gtdb_species": "s__Leptospira_A congkakensis", "ani": 85.083, "matched_fragments": 1062, "total_fragments": 1406, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004770905.1", "gtdb_species": "s__Leptospira_A bandrabouensis", "ani": 84.7267, "matched_fragments": 1053, "total_fragments": 1406, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004769235.1", "gtdb_species": "s__Leptospira_A kanakyensis", "ani": 84.5378, "matched_fragments": 1070, "total_fragments": 1406, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", 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"accession": "GCF_004770045.1", "gtdb_species": "s__Leptospira_A montravelensis", "ani": 84.2324, "matched_fragments": 1061, "total_fragments": 1406, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.8, "cell_length": 0.954, "doubling_h": 1.009, "growth_tmp": 29.0, "optimum_tmp": 30.329, "optimum_ph": 7.4, "genome_size": 4176292.667, "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", "meyeri" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }