{ "type": "genome", "identifier": "GCF_007992075.1", "organism": "Pararhodospirillum oryzae", "title": "Pararhodospirillum oryzae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation Biological Resource Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_007992075.1", "bioproject": "PRJNA224116", "biosample": "SAMD00172650", "wgs_master": "BJZO00000000.1", "refseq_category": "reference genome", "taxid": "478448", "species_taxid": "478448", "organism_name": "Pararhodospirillum oryzae", "infraspecific_name": "strain=NBRC 107573", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/31", "asm_name": "ASM799207v1", "asm_submitter": "National Institute of Technology and Evaluation Biological Resource Center", "gbrs_paired_asm": "GCA_007992075.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/007/992/075/GCF_007992075.1_ASM799207v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3832132", "genome_size_ungapped": "3832132", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "206", "contig_count": "206", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_007992075.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3330", "protein_coding_gene_count": "3246", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-31", "dateModified": "2019-07-31", "datePublished": "2019-07-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Pararhodospirillum oryzae" ], "sample_taxid": [ "478448" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India:Andhra Pradesh, Nadergul" ], "sample_host_location_id": [], "data_size": "1.058 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)": "3832132", "Number of Sequences": "206", "Longest Sequences (bp)": "98683", "N50 (bp)": "39047", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.0", "Number of CDSs": "3199", "Average Protein Length": "337.2", "Coding Ratio (%)": "84.4", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pararhodospirillum oryzae", "strain": "strain=NBRC 107573", "accession": "GCA_007992075.1", "taxid": 478448, "species_taxid": 478448, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1165, "total_fragments": 1176, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pararhodospirillum photometricum", "strain": "strain=DSM 122", "accession": "GCA_000284415.2", "taxid": 1084, "species_taxid": 1084, "relation_to_type": "type", "validated": true, "ani": 79.7233, "matched_fragments": 537, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodospirillum rubrum", "strain": "strain=DSM 467", "accession": "GCA_019134555.1", "taxid": 1085, "species_taxid": 1085, "relation_to_type": "type", "validated": true, "ani": 77.8635, "matched_fragments": 392, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodospirillum rubrum", "strain": "strain=ATCC 11170", "accession": "GCA_000013085.1", "taxid": 1085, "species_taxid": 1085, "relation_to_type": "type", "validated": true, "ani": 77.8583, "matched_fragments": 390, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phaeovibrio sulfidiphilus", "strain": "strain=DSM 23193", "accession": "GCA_014861485.1", "taxid": 1220600, "species_taxid": 1220600, "relation_to_type": "type", "validated": true, "ani": 77.8285, "matched_fragments": 196, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseospira goensis", "strain": "strain=JA135", "accession": "GCA_014197795.1", "taxid": 391922, "species_taxid": 391922, "relation_to_type": "type", "validated": true, "ani": 77.2019, "matched_fragments": 304, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Magnetospirillum marisnigri", "strain": "strain=SP-1", "accession": "GCA_001650715.1", "taxid": 1285242, "species_taxid": 1285242, "relation_to_type": "type", "validated": true, "ani": 76.9312, "matched_fragments": 228, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Magnetospirillum magnetotacticum", "strain": "strain=MS-1", "accession": "GCA_000829825.1", "taxid": 188, "species_taxid": 188, "relation_to_type": "type", "validated": true, "ani": 76.7248, "matched_fragments": 206, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vineibacter terrae", "strain": "strain=CC-CFT640", "accession": "GCA_008039615.1", "taxid": 2586908, "species_taxid": 2586908, "relation_to_type": "type", "validated": true, "ani": 76.1935, "matched_fragments": 186, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium goesingense", "strain": "strain=DSM 21331", "accession": "GCA_022179225.1", "taxid": 243690, "species_taxid": 243690, "relation_to_type": "type", "validated": true, "ani": 75.8942, "matched_fragments": 114, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodoligotrophos defluvii", "strain": "strain=lm1", "accession": "GCA_005281615.1", "taxid": 2561934, "species_taxid": 2561934, "relation_to_type": "type", "validated": true, "ani": 75.8105, "matched_fragments": 87, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Methylobacterium crusticola", "strain": "strain=KCTC 52305", "accession": "GCA_022179145.1", "taxid": 1697972, "species_taxid": 1697972, "relation_to_type": "type", "validated": true, "ani": 75.784, "matched_fragments": 199, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas folli", "strain": "strain=RHCKR7", "accession": "GCA_019429525.1", "taxid": 2862497, "species_taxid": 2862497, "relation_to_type": "type", "validated": true, "ani": 75.6454, "matched_fragments": 108, "total_fragments": 1176, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007992075.1", "gtdb_species": "s__Pararhodospirillum oryzae", "ani": 100.0, "matched_fragments": 1165, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum", "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_000284415.1", "gtdb_species": "s__Pararhodospirillum photometricum", "ani": 79.7325, "matched_fragments": 535, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum", "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_000013085.1", "gtdb_species": "s__Rhodospirillum rubrum", "ani": 77.8455, "matched_fragments": 391, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "96.31", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_014861485.1", "gtdb_species": "s__Phaeovibrio sulfidiphilus", "ani": 77.8285, "matched_fragments": 196, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Phaeovibrio", "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_009601025.1", "gtdb_species": "s__Rhodospira navarrensis", "ani": 77.6197, "matched_fragments": 285, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira", "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_900100455.1", "gtdb_species": "s__Roseospirillum parvum", "ani": 77.3835, "matched_fragments": 335, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Roseospirillum", "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_000961745.1", "gtdb_species": "s__BRH-c57 sp000961745", "ani": 77.2639, "matched_fragments": 192, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__BRH-c57", "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_014197915.1", "gtdb_species": "s__Rhodospira visakhapatnamensis", "ani": 77.2254, "matched_fragments": 301, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira", "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_014197795.1", "gtdb_species": "s__Rhodospira goensis", "ani": 77.1684, "matched_fragments": 308, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira", "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_902729435.1", "gtdb_species": "s__Magnetospirillum sp902729435", "ani": 77.0324, "matched_fragments": 260, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum", "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_001511835.1", "gtdb_species": "s__Phaeospirillum sp001511835", "ani": 77.0135, "matched_fragments": 269, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum", "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_000829825.1", "gtdb_species": "s__Phaeospirillum magnetotacticum", "ani": 76.7218, "matched_fragments": 205, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum", "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_003250275.1", "gtdb_species": "s__Alpha-05 sp003250275", "ani": 76.6157, "matched_fragments": 152, "total_fragments": 1176, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05", "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": 0.301, "cell_length": 1.0, "doubling_h": null, "growth_tmp": 26.75, "optimum_tmp": 30.0, "optimum_ph": 7.0, "genome_size": 3876289.25, "gc_content": 64.7, "coding_genes": 3201.333, "rRNA16S_genes": 1.0, "tRNA_genes": 93.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Pararhodospirillum", "oryzae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }