{ "type": "genome", "identifier": "GCF_000306255.2", "organism": "Leptospira noguchii serovar Panama str. CZ214", "title": "Leptospira noguchii serovar Panama str. CZ214", "description": "na", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000306255.2", "bioproject": "PRJNA224116", "biosample": "SAMN02436411", "wgs_master": "AKWY00000000.2", "refseq_category": "reference genome", "taxid": "1001595", "species_taxid": "28182", "organism_name": "Leptospira noguchii serovar Panama str. CZ214", "infraspecific_name": "strain=CZ214", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/08/07", "asm_name": "gls454059v02", "asm_submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "GCA_000306255.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/306/255/GCF_000306255.2_gls454059v02", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4710917", "genome_size_ungapped": "4710917", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000306255.2-RS_2024_03_21", "annotation_date": "2024-03-21", "total_gene_count": "4051", "protein_coding_gene_count": "3801", "non_coding_gene_count": "44", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-08-07", "dateModified": "2013-08-07", "datePublished": "2013-08-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira noguchii serovar Panama str. CZ214" ], "sample_taxid": [ "1001595" ], "sample_host_organism": [ "Didelphis marsupialis" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Panama: Canal Zone" ], "sample_host_location_id": [], "data_size": "1.314 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.38, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4710917", "Number of Sequences": "35", "Longest Sequences (bp)": "690650", "N50 (bp)": "280299", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.5", "Number of CDSs": "3969", "Average Protein Length": "306.3", "Coding Ratio (%)": "77.4", "Number of rRNAs": "5", "Number of tRNAs": "38", "Number of CRISPRs": "6" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira noguchii", "strain": "strain=CZ214", "accession": "GCA_000306255.2", "taxid": 28182, "species_taxid": 28182, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 1537, "total_fragments": 1554, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira kirschneri", "strain": "strain=3522 CT", "accession": "GCA_000243695.3", "taxid": 29507, "species_taxid": 29507, "relation_to_type": "type", "validated": true, "ani": 89.6421, "matched_fragments": 1282, "total_fragments": 1554, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira interrogans", "strain": "strain=RGA", "accession": "GCA_000343165.1", "taxid": 173, "species_taxid": 173, "relation_to_type": "type", "validated": true, "ani": 88.7815, "matched_fragments": 1257, "total_fragments": 1554, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira interrogans", "strain": "strain=ATCC 43642", "accession": "GCA_900156205.1", "taxid": 173, 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95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "97.03", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 36, "status": "-" }, { "accession": "GCF_900156205.1", "gtdb_species": "s__Leptospira interrogans", "ani": 88.7792, "matched_fragments": 1291, "total_fragments": 1554, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.34", "min_intra_species_ani": "97.40", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 353, "status": "-" }, { "accession": "GCF_000332415.1", "gtdb_species": "s__Leptospira weilii_A", "ani": 80.4208, "matched_fragments": 896, "total_fragments": 1554, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "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_000347175.1", "gtdb_species": "s__Leptospira alstonii", "ani": 80.3214, "matched_fragments": 903, "total_fragments": 1554, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.25", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000243815.2", "gtdb_species": "s__Leptospira alexanderi", "ani": 79.9788, "matched_fragments": 857, "total_fragments": 1554, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003046425.1", "gtdb_species": "s__Leptospira borgpetersenii", "ani": 79.7941, "matched_fragments": 812, "total_fragments": 1554, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "97.82", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 148, "status": "-" }, { "accession": "GCF_002811925.1", "gtdb_species": "s__Leptospira barantonii", "ani": 79.5627, "matched_fragments": 708, "total_fragments": 1554, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.36", "min_intra_species_ani": "96.36", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -1.0, "cell_length": 0.778, "doubling_h": 1.009, "growth_tmp": 29.0, "optimum_tmp": 29.0, "optimum_ph": 7.4, "genome_size": 4696906.467, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Leptospira", "noguchii", "serovar", "Panama", "str.", "CZ214" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }