{ "type": "genome", "identifier": "GCF_014205765.1", "organism": "Nitrospirillum iridis", "title": "Nitrospirillum iridis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014205765.1", "bioproject": "PRJNA224116", "biosample": "SAMN12025536", "wgs_master": "JACIIZ000000000.1", "refseq_category": "reference genome", "taxid": "765888", "species_taxid": "765888", "organism_name": "Nitrospirillum iridis", "infraspecific_name": "strain=DSM 22198", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1420576v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014205765.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/205/765/GCF_014205765.1_ASM1420576v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7088717", "genome_size_ungapped": "7088335", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "54", "contig_count": "54", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014205765.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "6023", "protein_coding_gene_count": "5914", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Nitrospirillum iridis" ], "sample_taxid": [ "765888" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.940 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)": "7088717", "Number of Sequences": "54", "Longest Sequences (bp)": "684039", "N50 (bp)": "303652", "Gap Ratio (%)": "0.005389", "GCcontent (%)": "67.2", "Number of CDSs": "6013", "Average Protein Length": "345.7", "Coding Ratio (%)": "88.0", "Number of rRNAs": "1", "Number of tRNAs": "61", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nitrospirillum iridis", "strain": "strain=DSM 22198", "accession": "GCA_014205765.1", "taxid": 765888, "species_taxid": 765888, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2340, "total_fragments": 2341, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Azospirillum formosense", "strain": "strain=CC-NFb-7", "accession": "GCA_013340925.1", "taxid": 861533, "species_taxid": 861533, "relation_to_type": "type", "validated": true, "ani": 78.0061, "matched_fragments": 476, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum rugosum", "strain": "strain=IMMIB AFH-6", "accession": "GCA_017876155.1", "taxid": 416170, "species_taxid": 416170, "relation_to_type": "type", "validated": true, "ani": 77.9994, "matched_fragments": 621, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum soli", "strain": "strain=CC-LY788", "accession": "GCA_017876165.1", "taxid": 1304799, "species_taxid": 1304799, "relation_to_type": "type", "validated": true, "ani": 77.9824, "matched_fragments": 528, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum humicireducens", "strain": "strain=SgZ-5", "accession": "GCA_001639105.2", "taxid": 1226968, "species_taxid": 1226968, "relation_to_type": "type", "validated": true, "ani": 77.9576, "matched_fragments": 556, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niveispirillum cyanobacteriorum", "strain": "strain=TH16", "accession": "GCA_002868735.1", "taxid": 1612173, "species_taxid": 1612173, "relation_to_type": "type", "validated": true, "ani": 77.9006, "matched_fragments": 510, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum baldaniorum", "strain": "strain=Sp245", "accession": "GCA_003119195.2", "taxid": 1064539, "species_taxid": 1064539, "relation_to_type": "type", "validated": true, "ani": 77.8906, "matched_fragments": 579, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum oryzae", "strain": "strain=COC8", "accession": "GCA_008364795.1", "taxid": 286727, "species_taxid": 286727, "relation_to_type": "type", "validated": true, "ani": 77.868, "matched_fragments": 587, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum baldaniorum", "strain": "strain=Sp245", "accession": "GCA_000237365.1", "taxid": 1064539, "species_taxid": 1064539, "relation_to_type": "type", "validated": true, "ani": 77.8582, "matched_fragments": 574, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niveispirillum cyanobacteriorum", "strain": "strain=CGMCC 1.12958", "accession": "GCA_014640215.1", "taxid": 1612173, "species_taxid": 1612173, "relation_to_type": "type", "validated": true, "ani": 77.8515, "matched_fragments": 505, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum thermophilum", "strain": "strain=CFH 70021", "accession": "GCA_003130795.1", "taxid": 2202148, "species_taxid": 2202148, "relation_to_type": "type", "validated": true, "ani": 77.8294, "matched_fragments": 593, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum argentinense", "strain": "strain=Az39", "accession": "GCA_000632475.2", "taxid": 2970906, "species_taxid": 2970906, "relation_to_type": "type", "validated": true, "ani": 77.8185, "matched_fragments": 581, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum oleiclasticum", "strain": "strain=RWY-5-1-1", "accession": "GCA_013423485.1", "taxid": 2735135, "species_taxid": 2735135, "relation_to_type": "type", "validated": true, "ani": 77.7314, "matched_fragments": 588, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum halopraeferens", "strain": "strain=DSM 3675", "accession": "GCA_000429625.1", "taxid": 34010, "species_taxid": 34010, "relation_to_type": "type", "validated": true, "ani": 77.7226, "matched_fragments": 597, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella rosea", "strain": "strain=KEMB 2255-458", "accession": "GCA_016806835.2", "taxid": 1817965, "species_taxid": 1817965, "relation_to_type": "type", "validated": true, "ani": 77.7023, "matched_fragments": 505, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella mucosa", "strain": "strain=KEMB 2255-438", "accession": "GCA_016765655.2", "taxid": 1789672, "species_taxid": 1789672, "relation_to_type": "type", "validated": true, "ani": 77.6967, "matched_fragments": 481, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum agricola", "strain": "strain=CC-HIH038", "accession": "GCA_017876095.1", "taxid": 1720247, "species_taxid": 1720247, "relation_to_type": "type", "validated": true, "ani": 77.6176, "matched_fragments": 617, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Skermanella stibiiresistens", "strain": "strain=SB22", "accession": "GCA_000576635.1", "taxid": 913326, "species_taxid": 913326, "relation_to_type": "type", "validated": true, "ani": 77.4221, "matched_fragments": 450, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum cavernae", "strain": "strain=K2W22B-5", "accession": "GCA_003590795.1", "taxid": 2320860, "species_taxid": 2320860, "relation_to_type": "type", "validated": true, "ani": 77.3683, "matched_fragments": 430, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arenibaculum pallidiluteum", "strain": "strain=SYSU D00532", "accession": "GCA_017355985.1", "taxid": 2812559, "species_taxid": 2812559, "relation_to_type": "type", "validated": true, "ani": 77.253, "matched_fragments": 400, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseococcus pinisoli", "strain": "strain=XZZS9", "accession": "GCA_018413645.1", "taxid": 2835040, "species_taxid": 2835040, "relation_to_type": "type", "validated": true, "ani": 76.3223, "matched_fragments": 277, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas haemaphysalidis", "strain": "strain=546", "accession": "GCA_017355405.1", "taxid": 2768162, "species_taxid": 2768162, "relation_to_type": "type", "validated": true, "ani": 76.2865, "matched_fragments": 366, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseococcus microcysteis", "strain": "strain=NIBR12", "accession": "GCA_014764365.1", "taxid": 2771361, "species_taxid": 2771361, "relation_to_type": "type", "validated": true, "ani": 76.0254, "matched_fragments": 292, "total_fragments": 2341, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014205765.1", "gtdb_species": "s__Nitrospirillum iridis", "ani": 100.0, "matched_fragments": 2340, "total_fragments": 2341, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum", "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_000333275.1", "gtdb_species": "s__Nitrospirillum sp000333275", "ani": 87.8466, "matched_fragments": 1555, "total_fragments": 2341, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum", "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_007828045.1", "gtdb_species": "s__Nitrospirillum amazonense_C", "ani": 87.3827, "matched_fragments": 1705, "total_fragments": 2341, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum", "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_000730165.1", "gtdb_species": "s__Nitrospirillum amazonense", "ani": 87.2544, "matched_fragments": 1747, "total_fragments": 2341, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.38", "min_intra_species_ani": "95.62", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_007828035.1", "gtdb_species": "s__Nitrospirillum amazonense_A", "ani": 87.2327, "matched_fragments": 1714, "total_fragments": 2341, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum", "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_007827955.1", "gtdb_species": "s__Nitrospirillum amazonense_B", "ani": 86.9017, "matched_fragments": 1670, "total_fragments": 2341, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum", "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": null, "cell_length": null, "doubling_h": 1.0, "growth_tmp": 30.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 7138782.4, "gc_content": 67.148, "coding_genes": 6076.0, "rRNA16S_genes": 5.0, "tRNA_genes": 63.0, "gram_stain": 0.0, "sporulation": null, "motility": 1.0, "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": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Nitrospirillum", "iridis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }