{ "type": "genome", "identifier": "GCF_000332455.1", "organism": "Leptospira vanthielii serovar Holland str. Waz Holland = ATCC 700522", "title": "Leptospira vanthielii serovar Holland str. Waz Holland = ATCC 700522", "description": "na", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000332455.1", "bioproject": "PRJNA224116", "biosample": "SAMN02436568", "wgs_master": "AOGY00000000.2", "refseq_category": "na", "taxid": "1218591", "species_taxid": "293085", "organism_name": "Leptospira vanthielii serovar Holland str. Waz Holland = ATCC 700522", "infraspecific_name": "strain=Waz Holland", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/08", "asm_name": "gls454199v02", "asm_submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "GCA_000332455.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/332/455/GCF_000332455.1_gls454199v02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4232327", "genome_size_ungapped": "4232327", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "89", "contig_count": "89", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-16", "total_gene_count": "4125", "protein_coding_gene_count": "4006", "non_coding_gene_count": "46", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-08", "dateModified": "2013-04-08", "datePublished": "2013-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira vanthielii serovar Holland str. Waz Holland = ATCC 700522" ], "sample_taxid": [ "1218591" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Netherlands" ], "sample_host_location_id": [], "data_size": "1.197 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)": "4232327", "Number of Sequences": "89", "Longest Sequences (bp)": "428074", "N50 (bp)": "164554", "Gap Ratio (%)": "0.000047", "GCcontent (%)": "38.9", "Number of CDSs": "4004", "Average Protein Length": "315.5", "Coding Ratio (%)": "89.6", "Number of rRNAs": "4", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira vanthielii", "strain": "strain=Waz Holland", "accession": "GCA_000332455.2", "taxid": 293085, "species_taxid": 293085, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1363, "total_fragments": 1368, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira wolbachii", "strain": "strain=CDC", "accession": "GCA_000332515.2", "taxid": 29511, "species_taxid": 29511, "relation_to_type": "type", "validated": true, "ani": 90.0882, "matched_fragments": 1207, "total_fragments": 1368, "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": 89.6469, "matched_fragments": 1150, "total_fragments": 1368, "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": 86.2887, "matched_fragments": 1153, "total_fragments": 1368, "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": 85.9185, "matched_fragments": 1069, "total_fragments": 1368, "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": 83.569, "matched_fragments": 1029, "total_fragments": 1368, "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": 83.3145, "matched_fragments": 1039, "total_fragments": 1368, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000332455.1", "gtdb_species": "s__Leptospira_A vanthielii", "ani": 100.0, "matched_fragments": 1363, "total_fragments": 1368, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "98.49", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000332515.2", "gtdb_species": "s__Leptospira_A wolbachii", "ani": 90.0919, "matched_fragments": 1207, "total_fragments": 1368, "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_016918735.1", "gtdb_species": "s__Leptospira_A sp016918735", "ani": 89.6612, "matched_fragments": 1148, "total_fragments": 1368, "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_000332495.1", "gtdb_species": "s__Leptospira_A terpstrae", "ani": 86.3174, "matched_fragments": 1151, "total_fragments": 1368, "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_016919165.1", "gtdb_species": "s__Leptospira_A sp016919165", "ani": 85.9495, "matched_fragments": 1067, "total_fragments": 1368, "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": "-" } ] }, "_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", "vanthielii", "serovar", "Holland", "str.", "Waz", "Holland", "=", "ATCC", "700522" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }