{ "type": "genome", "identifier": "GCF_002811945.1", "organism": "Leptospira harrisiae", "title": "Leptospira harrisiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institut Pasteur Montevideo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002811945.1", "bioproject": "PRJNA224116", "biosample": "SAMN07411419", "wgs_master": "NPDX00000000.1", "refseq_category": "reference genome", "taxid": "2023189", "species_taxid": "2023189", "organism_name": "Leptospira harrisiae", "infraspecific_name": "strain=FH2-B-A1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/12/05", "asm_name": "ASM281194v1", "asm_submitter": "Institut Pasteur Montevideo", "gbrs_paired_asm": "GCA_002811945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/811/945/GCF_002811945.1_ASM281194v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3946761", "genome_size_ungapped": "3946522", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "17", "contig_count": "17", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002811945.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "3684", "protein_coding_gene_count": "3626", "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 harrisiae" ], "sample_taxid": [ "2023189" ], "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": "1.110 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)": "3946761", "Number of Sequences": "17", "Longest Sequences (bp)": "2088660", "N50 (bp)": "2088660", "Gap Ratio (%)": "0.006056", "GCcontent (%)": "37.9", "Number of CDSs": "3648", "Average Protein Length": "333.1", "Coding Ratio (%)": "92.4", "Number of rRNAs": "5", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1308, "total_fragments": 1308, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira meyeri", "strain": "strain=DSM 21537", "accession": "GCA_004368965.1", "taxid": 29508, "species_taxid": 29508, "relation_to_type": "type", "validated": true, "ani": 85.9419, "matched_fragments": 1154, "total_fragments": 1308, "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": 83.6478, "matched_fragments": 1005, "total_fragments": 1308, "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": 83.6267, "matched_fragments": 1014, "total_fragments": 1308, "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": 83.6128, "matched_fragments": 1013, "total_fragments": 1308, "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": 83.5661, "matched_fragments": 1051, "total_fragments": 1308, "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": 83.5583, "matched_fragments": 1042, "total_fragments": 1308, "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": 83.4124, "matched_fragments": 999, "total_fragments": 1308, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002811945.1", "gtdb_species": "s__Leptospira_A harrisiae", "ani": 100.0, "matched_fragments": 1308, "total_fragments": 1308, "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": "conclusive" }, { "accession": "GCF_004770475.1", "gtdb_species": "s__Leptospira_A mtsangambouensis", "ani": 87.2826, "matched_fragments": 1171, "total_fragments": 1308, "gtdb_taxonomy": 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"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": "-" }, { "accession": "GCF_004368965.1", "gtdb_species": "s__Leptospira_A meyeri", "ani": 85.9419, "matched_fragments": 1154, "total_fragments": 1308, "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": "-" }, { "accession": "GCF_004770765.1", "gtdb_species": "s__Leptospira_A noumeaensis", "ani": 85.9348, "matched_fragments": 1045, "total_fragments": 1308, "gtdb_taxonomy": 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"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_000332515.2", "gtdb_species": "s__Leptospira_A wolbachii", "ani": 83.6242, "matched_fragments": 1011, "total_fragments": 1308, "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, 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