{ "type": "genome", "identifier": "GCF_001311845.1", "organism": "Desulfosarcina cetonica JCM 12296", "title": "Desulfosarcina cetonica JCM 12296", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001311845.1", "bioproject": "PRJNA224116", "biosample": "SAMD00000427", "wgs_master": "BBCC00000000.1", "refseq_category": "reference genome", "taxid": "1294021", "species_taxid": "90730", "organism_name": "Desulfosarcina cetonica JCM 12296", "infraspecific_name": "strain=JCM 12296", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/10/02", "asm_name": "ASM131184v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_001311845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/311/845/GCF_001311845.1_ASM131184v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7092334", "genome_size_ungapped": "7092334", "gc_percent": "55.500000", "replicon_count": "0", "scaffold_count": "558", "contig_count": "558", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001311845.1-RS_2024_04_07", "annotation_date": "2024-04-07", "total_gene_count": "7919", "protein_coding_gene_count": "7404", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-10-02", "dateModified": "2015-10-02", "datePublished": "2015-10-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Desulfosarcina cetonica JCM 12296" ], "sample_taxid": [ "1294021" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "NA" ], "sample_host_location_id": [], "data_size": "2.017 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7092334", "Number of Sequences": "558", "Longest Sequences (bp)": "114531", "N50 (bp)": "28138", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.7", "Number of CDSs": "7306", "Average Protein Length": "258.2", "Coding Ratio (%)": "79.8", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Desulfosarcina cetonica", "strain": "strain=JCM 12296", "accession": "GCA_001311845.1", "taxid": 90730, "species_taxid": 90730, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2083, "total_fragments": 2103, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Desulfosarcina ovata subsp. sediminis", "strain": "strain=28bB2T", "accession": "GCA_009688985.1", "taxid": 885957, "species_taxid": 83564, "relation_to_type": "type", "validated": true, "ani": 81.4301, "matched_fragments": 1064, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfosarcina ovata subsp. ovata", "strain": "strain=oXyS1", "accession": "GCA_009689005.1", "taxid": 2752305, "species_taxid": 83564, "relation_to_type": "type", "validated": true, "ani": 80.9342, "matched_fragments": 998, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfosarcina widdelii", "strain": "strain=PP31", "accession": "GCA_009688965.1", "taxid": 947919, "species_taxid": 947919, "relation_to_type": "type", "validated": true, "ani": 78.4181, "matched_fragments": 532, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfosarcina alkanivorans", "strain": "strain=PL12", "accession": "GCA_009688945.1", "taxid": 571177, "species_taxid": 571177, "relation_to_type": "type", "validated": true, "ani": 78.0492, "matched_fragments": 546, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfococcus multivorans", "strain": "strain=DSM 2059", "accession": "GCA_900167235.1", "taxid": 897, "species_taxid": 897, "relation_to_type": "type", "validated": true, "ani": 76.5587, "matched_fragments": 105, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfonema ishimotonii", "strain": "strain=Tokyo 01", "accession": "GCA_003851005.1", "taxid": 45657, "species_taxid": 45657, "relation_to_type": "type", "validated": true, "ani": 76.5101, "matched_fragments": 115, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfotignum phosphitoxidans", "strain": "strain=DSM 13687", "accession": "GCA_000350545.1", "taxid": 190898, "species_taxid": 190898, "relation_to_type": "type", "validated": true, "ani": 76.0091, "matched_fragments": 75, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Desulfacinum infernum", "strain": "strain=DSM 9756", "accession": "GCA_900129305.1", "taxid": 35837, "species_taxid": 35837, "relation_to_type": "type", "validated": true, "ani": 75.7468, "matched_fragments": 56, "total_fragments": 2103, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001311845.1", "gtdb_species": "s__Desulfosarcina cetonica", "ani": 100.0, "matched_fragments": 2083, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.91", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_009689005.1", "gtdb_species": "s__Desulfosarcina ovata", "ani": 80.8571, "matched_fragments": 1012, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.03", "min_intra_species_ani": "97.03", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.77", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009688965.1", "gtdb_species": "s__Desulfosarcina widdelii", "ani": 78.3897, "matched_fragments": 536, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "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": "GCA_014237405.1", "gtdb_species": "s__Desulfosarcina sp014237405", "ani": 78.079, "matched_fragments": 380, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.69", "min_intra_species_ani": "99.69", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009688945.1", "gtdb_species": "s__Desulfosarcina alkanivorans", "ani": 78.0388, "matched_fragments": 547, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "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": "GCA_018224455.1", "gtdb_species": "s__Desulfosarcina sp018224455", "ani": 77.934, "matched_fragments": 313, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "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": "GCA_002352605.1", "gtdb_species": "s__Desulfosarcina sp002352605", "ani": 77.8636, "matched_fragments": 264, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "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": "GCA_011390985.1", "gtdb_species": "s__JAABRJ01 sp011390985", "ani": 77.2136, "matched_fragments": 102, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAABRJ01;g__JAABRJ01", "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": "GCA_002747175.1", "gtdb_species": "s__Desulfosarcina sp002747175", "ani": 77.0487, "matched_fragments": 108, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.81", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.57", "min_intra_species_af": "0.57", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018224505.1", "gtdb_species": "s__Desulfatitalea sp018224505", "ani": 76.7994, "matched_fragments": 124, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfatitalea", "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": "GCA_018335195.1", "gtdb_species": "s__Desulfosalsimonas sp018335195", "ani": 75.9531, "matched_fragments": 67, "total_fragments": 2103, "gtdb_taxonomy": "d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__Desulfosalsimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.35", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 7039684.0, "gc_content": 55.2, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Desulfosarcina", "cetonica", "JCM", "12296" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }