{ "type": "genome", "identifier": "GCF_000347175.1", "organism": "Leptospira alstonii serovar Sichuan str. 79601", "title": "Leptospira alstonii serovar Sichuan str. 79601", "description": "na", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000347175.1", "bioproject": "PRJNA224116", "biosample": "SAMN01801604", "wgs_master": "ANIK00000000.1", "refseq_category": "reference genome", "taxid": "1218565", "species_taxid": "28452", "organism_name": "Leptospira alstonii serovar Sichuan str. 79601", "infraspecific_name": "strain=79601", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/03/15", "asm_name": "gls454194v01", "asm_submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "GCA_000347175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/347/175/GCF_000347175.1_gls454194v01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4436408", "genome_size_ungapped": "4436408", "gc_percent": "42.500000", "replicon_count": "0", "scaffold_count": "125", "contig_count": "125", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000347175.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "4102", "protein_coding_gene_count": "3864", "non_coding_gene_count": "46", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-03-15", "dateModified": "2013-03-15", "datePublished": "2013-03-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Leptospira alstonii serovar Sichuan str. 79601" ], "sample_taxid": [ "1218565" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.250 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)": "4436408", "Number of Sequences": "125", "Longest Sequences (bp)": "295179", "N50 (bp)": "68494", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.5", "Number of CDSs": "3892", "Average Protein Length": "312.3", "Coding Ratio (%)": "82.2", "Number of rRNAs": "7", "Number of tRNAs": "37", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Leptospira alstonii", "strain": "strain=79601", "accession": "GCA_000347175.1", "taxid": 28452, "species_taxid": 28452, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1410, "total_fragments": 1416, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Leptospira alexanderi", "strain": "strain=L 60", "accession": "GCA_000243815.3", "taxid": 100053, "species_taxid": 100053, "relation_to_type": "type", "validated": true, "ani": 83.7773, "matched_fragments": 1036, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira santarosai", "strain": "strain=LT 821", "accession": "GCA_000313175.2", "taxid": 28183, "species_taxid": 28183, "relation_to_type": "type", "validated": true, "ani": 82.9633, "matched_fragments": 969, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira kmetyi", "strain": "strain=Bejo-Iso9", "accession": "GCA_000243735.3", "taxid": 408139, "species_taxid": 408139, "relation_to_type": "type", "validated": true, "ani": 82.895, "matched_fragments": 959, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira mayottensis", "strain": "strain=200901116", "accession": "GCA_000306675.3", "taxid": 1137606, "species_taxid": 1137606, "relation_to_type": "type", "validated": true, "ani": 82.766, "matched_fragments": 998, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira borgpetersenii", "strain": "strain=DSM 21538", "accession": "GCA_003046425.1", "taxid": 174, "species_taxid": 174, "relation_to_type": "type", "validated": true, "ani": 82.6253, "matched_fragments": 976, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira barantonii", "strain": "strain=FH4-C-A1", "accession": "GCA_002811925.1", "taxid": 2023184, "species_taxid": 2023184, "relation_to_type": "type", "validated": true, "ani": 82.4991, "matched_fragments": 951, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira yasudae", "strain": "strain=F1", "accession": "GCA_003545925.1", "taxid": 2202201, "species_taxid": 2202201, "relation_to_type": "type", "validated": true, "ani": 81.7904, "matched_fragments": 924, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira tipperaryensis", "strain": "strain=GWTS #1", "accession": "GCA_001729245.1", "taxid": 2564040, "species_taxid": 2564040, "relation_to_type": "type", "validated": true, "ani": 80.5853, "matched_fragments": 817, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira adleri", "strain": "strain=FH2-B-D1", "accession": "GCA_002811985.1", "taxid": 2023186, "species_taxid": 2023186, "relation_to_type": "type", "validated": true, "ani": 80.5851, "matched_fragments": 762, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira ainlahdjerensis", "strain": "strain=201903070", "accession": "GCA_016919175.1", "taxid": 2810033, "species_taxid": 2810033, "relation_to_type": "type", "validated": true, "ani": 80.3153, "matched_fragments": 767, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leptospira ellisii", "strain": "strain=ATI7-C-A5", "accession": "GCA_002811955.1", "taxid": 2023197, "species_taxid": 2023197, "relation_to_type": "type", "validated": true, "ani": 79.6246, "matched_fragments": 582, "total_fragments": 1416, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000347175.1", "gtdb_species": "s__Leptospira alstonii", "ani": 100.0, "matched_fragments": 1410, "total_fragments": 1416, "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": "conclusive" }, { "accession": "GCF_000332415.1", "gtdb_species": "s__Leptospira weilii_A", "ani": 91.381, "matched_fragments": 1171, "total_fragments": 1416, "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_000243815.2", "gtdb_species": "s__Leptospira alexanderi", "ani": 83.8087, "matched_fragments": 1032, "total_fragments": 1416, "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_000244815.1", "gtdb_species": "s__Leptospira weilii", "ani": 83.2966, "matched_fragments": 1025, "total_fragments": 1416, "gtdb_taxonomy": "d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.50", "min_intra_species_ani": "95.12", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.84", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_000313175.2", "gtdb_species": "s__Leptospira santarosai", "ani": 82.9874, "matched_fragments": 964, "total_fragments": 1416, "gtdb_taxonomy": 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