{ "type": "genome", "identifier": "GCF_011601265.1", "organism": "Iodobacter violaceini", "title": "Iodobacter violaceini", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Sierra College", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011601265.1", "bioproject": "PRJNA224116", "biosample": "SAMN13942217", "wgs_master": "JAAOLX000000000.1", "refseq_category": "reference genome", "taxid": "3044271", "species_taxid": "3044271", "organism_name": "Iodobacter violaceini", "infraspecific_name": "strain=HSC-16F04", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/20", "asm_name": "ASM1160126v1", "asm_submitter": "Sierra College", "gbrs_paired_asm": "GCA_011601265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/601/265/GCF_011601265.1_ASM1160126v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4784879", "genome_size_ungapped": "4784879", "gc_percent": "49.500000", "replicon_count": "0", "scaffold_count": "68", "contig_count": "68", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011601265.1-RS_2024_08_12", "annotation_date": "2024-08-12", "total_gene_count": "4396", "protein_coding_gene_count": "4280", "non_coding_gene_count": "90", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-20", "dateModified": "2020-03-20", "datePublished": "2020-03-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Iodobacter violaceini" ], "sample_taxid": [ "3044271" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: California, Ophir" ], "sample_host_location_id": [], "data_size": "1.353 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)": "4784879", "Number of Sequences": "68", "Longest Sequences (bp)": "787080", "N50 (bp)": "385521", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.4", "Number of CDSs": "4252", "Average Protein Length": "322.0", "Coding Ratio (%)": "85.8", "Number of rRNAs": "2", "Number of tRNAs": "76", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Iodobacter fluviatilis", "strain": "strain=DSM 3764", "accession": "GCA_004346505.1", "taxid": 537, "species_taxid": 537, "relation_to_type": "type", "validated": true, "ani": 92.0904, "matched_fragments": 1400, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Iodobacter fluviatilis", "strain": "strain=NCTC11159", "accession": "GCA_900451195.1", "taxid": 537, "species_taxid": 537, "relation_to_type": "type", "validated": true, "ani": 92.0514, "matched_fragments": 1428, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Iodobacter ciconiae", "strain": "strain=H11R3", "accession": "GCA_003952345.1", "taxid": 2496266, "species_taxid": 2496266, "relation_to_type": "type", "validated": true, "ani": 84.7793, "matched_fragments": 983, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinibacter tainanensis", "strain": "strain=DSM 15459", "accession": "GCA_000429785.1", "taxid": 230667, "species_taxid": 230667, "relation_to_type": "type", "validated": true, "ani": 77.1276, "matched_fragments": 177, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deefgea salmonis", "strain": "strain=H3-26", "accession": "GCA_020531905.1", "taxid": 2875502, "species_taxid": 2875502, "relation_to_type": "type", "validated": true, "ani": 77.0758, "matched_fragments": 152, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinibacter fontanus", "strain": "strain=STM-7", "accession": "GCA_013423785.1", "taxid": 1737446, "species_taxid": 1737446, "relation_to_type": "type", "validated": true, "ani": 76.9303, "matched_fragments": 149, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Deefgea rivuli", "strain": "strain=DSM 18356", "accession": "GCA_000620145.1", "taxid": 400948, "species_taxid": 400948, "relation_to_type": "type", "validated": true, "ani": 76.6619, "matched_fragments": 148, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Silvimonas amylolytica", "strain": "strain=CGMCC 1.8860", "accession": "GCA_014645555.1", "taxid": 449663, "species_taxid": 449663, "relation_to_type": "type", "validated": true, "ani": 76.5311, "matched_fragments": 131, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Silvimonas iriomotensis", "strain": "strain=CGMCC 1.8859", "accession": "GCA_014645535.1", "taxid": 449662, "species_taxid": 449662, "relation_to_type": "type", "validated": true, "ani": 76.528, "matched_fragments": 131, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinilyticum aquatile", "strain": "strain=DSM 21506", "accession": "GCA_000430805.1", "taxid": 362520, "species_taxid": 362520, "relation_to_type": "type", "validated": true, "ani": 76.2775, "matched_fragments": 101, "total_fragments": 1576, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011601265.1", "gtdb_species": "s__Iodobacter sp011601265", "ani": 100.0, "matched_fragments": 1573, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter", "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": "conclusive" }, { "accession": "GCF_002735645.1", "gtdb_species": "s__Iodobacter sp002735645", "ani": 94.8885, "matched_fragments": 1310, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter", "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_900451195.1", "gtdb_species": "s__Iodobacter fluviatilis", "ani": 92.0637, "matched_fragments": 1427, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter", "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_000969645.2", "gtdb_species": "s__Iodobacter sp000969645", "ani": 85.4487, "matched_fragments": 1203, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter", "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_003952345.1", "gtdb_species": "s__Iodobacter sp003952345", "ani": 84.764, "matched_fragments": 985, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter", "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_004194535.1", "gtdb_species": "s__Iodobacter fluviatilis_A", "ani": 82.5157, "matched_fragments": 903, "total_fragments": 1576, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter", "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": -0.19, "cell_length": 0.254, "doubling_h": null, "growth_tmp": 22.666, "optimum_tmp": 18.0, "optimum_ph": 8.25, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": null, "motility": 0.5, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Iodobacter", "violaceini" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }