{ "type": "genome", "identifier": "GCF_002812045.1", "organism": "Leptospira haakeii", "title": "Leptospira haakeii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institut Pasteur Montevideo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002812045.1", "bioproject": "PRJNA224116", "biosample": "SAMN07411410", "wgs_master": "NPEG00000000.1", "refseq_category": "na", "taxid": "2023198", "species_taxid": "2023198", "organism_name": "Leptospira haakeii", "infraspecific_name": "strain=ATI7-C-A4", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/12/05", "asm_name": "ASM281204v1", "asm_submitter": "Institut Pasteur Montevideo", "gbrs_paired_asm": "GCA_002812045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/812/045/GCF_002812045.1_ASM281204v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4191261", "genome_size_ungapped": "4191261", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "39", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002812045.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "3868", "protein_coding_gene_count": "3792", "non_coding_gene_count": "42", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-12-05", "dateModified": "2017-12-05", "datePublished": "2017-12-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira haakeii" ], "sample_taxid": [ "2023198" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "New Caledonia" ], "sample_host_location_id": [], "data_size": "1.183 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)": "4191261", "Number of Sequences": "39", "Longest Sequences (bp)": "1177136", "N50 (bp)": "236721", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.8", "Number of CDSs": "3791", "Average Protein Length": "333.6", "Coding Ratio (%)": "90.5", "Number of rRNAs": "4", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira haakeii", "strain": "strain=ATI7-C-A4", "accession": "GCA_002812045.1", "taxid": 2023198, "species_taxid": 2023198, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1378, "total_fragments": 1379, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira selangorensis", "strain": "strain=SSW17", "accession": "GCA_004769405.1", "taxid": 2484982, "species_taxid": 2484982, "relation_to_type": "type", "validated": true, "ani": 91.8969, "matched_fragments": 1312, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira saintgironsiae", "strain": "strain=FH4-C-A2", "accession": "GCA_002811765.1", "taxid": 2023183, "species_taxid": 2023183, "relation_to_type": "type", "validated": true, "ani": 89.5222, "matched_fragments": 1229, "total_fragments": 1379, "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": 88.0845, "matched_fragments": 1209, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira venezuelensis", "strain": "strain=CLM-U50", "accession": "GCA_002150035.1", "taxid": 1958811, "species_taxid": 1958811, "relation_to_type": "type", "validated": true, "ani": 87.8334, "matched_fragments": 1217, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira neocaledonica", "strain": "strain=ES4-C-A1", "accession": "GCA_002812205.1", "taxid": 2023192, "species_taxid": 2023192, "relation_to_type": "type", "validated": true, "ani": 87.6554, "matched_fragments": 1219, "total_fragments": 1379, "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": 87.3978, "matched_fragments": 1205, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira licerasiae", "strain": "strain=VAR 010", "accession": "GCA_000244755.3", "taxid": 447106, "species_taxid": 447106, "relation_to_type": "type", "validated": true, "ani": 87.0705, "matched_fragments": 1190, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira licerasiae", "strain": "strain=ATCC BAA-1110", "accession": "GCA_000526875.1", "taxid": 447106, "species_taxid": 447106, "relation_to_type": "type", "validated": true, "ani": 87.0509, "matched_fragments": 1212, "total_fragments": 1379, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002812045.1", "gtdb_species": "s__Leptospira_B haakeii", "ani": 100.0, "matched_fragments": 1378, "total_fragments": 1379, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_004769405.1", "gtdb_species": "s__Leptospira_B selangorensis", "ani": 91.8968, "matched_fragments": 1312, "total_fragments": 1379, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.97", "min_intra_species_ani": "97.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002811765.1", "gtdb_species": "s__Leptospira_B saintgironsiae", "ani": 89.5123, "matched_fragments": 1230, "total_fragments": 1379, "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_004770105.1", "gtdb_species": "s__Leptospira_B andrefontaineae", "ani": 89.4237, "matched_fragments": 1236, "total_fragments": 1379, "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_004770895.1", "gtdb_species": "s__Leptospira_B dzoumogneensis", "ani": 89.2145, "matched_fragments": 1257, "total_fragments": 1379, "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_004769555.1", "gtdb_species": "s__Leptospira_B koniambonensis", "ani": 88.9742, "matched_fragments": 1263, "total_fragments": 1379, "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": 88.0956, "matched_fragments": 1208, "total_fragments": 1379, "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", 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}, { "accession": "GCF_000347035.1", "gtdb_species": "s__Leptospira_B sp000347035", "ani": 85.8159, "matched_fragments": 1197, "total_fragments": 1379, "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": "-" } ] }, "_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", "haakeii" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }