{ "type": "genome", "identifier": "GCF_030814845.1", "organism": "Azospirillum rugosum", "title": "Azospirillum rugosum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_030814845.1", "bioproject": "PRJNA224116", "biosample": "SAMN35367913", "wgs_master": "JAUSVT000000000.1", "refseq_category": "reference genome", "taxid": "416170", "species_taxid": "416170", "organism_name": "Azospirillum rugosum", "infraspecific_name": "strain=DSM 19657", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/08/18", "asm_name": "ASM3081484v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_030814845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/814/845/GCF_030814845.1_ASM3081484v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "7559751", "genome_size_ungapped": "7559751", "gc_percent": "69.000000", "replicon_count": "0", "scaffold_count": "70", "contig_count": "70", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_030814845.1-RS_2024_08_20", "annotation_date": "2024-08-20", "total_gene_count": "6889", "protein_coding_gene_count": "6766", "non_coding_gene_count": "80", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-08-18", "dateModified": "2023-08-18", "datePublished": "2023-08-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Azospirillum rugosum" ], "sample_taxid": [ "416170" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Taiwan" ], "sample_host_location_id": [], "data_size": "2.053 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 50.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "7559751", "Number of Sequences": "70", "Longest Sequences (bp)": "416346", "N50 (bp)": "215041", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.9", "Number of CDSs": "6913", "Average Protein Length": "321.8", "Coding Ratio (%)": "88.3", "Number of rRNAs": "1", "Number of tRNAs": "85", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 99.9965, "matched_fragments": 2474, "total_fragments": 2484, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Azospirillum tabaci", "strain": "strain=W712", "accession": "GCA_014596085.1", "taxid": 2752310, "species_taxid": 2752310, "relation_to_type": "type", "validated": true, "ani": 86.1791, "matched_fragments": 1511, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" }, { "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": 86.1688, "matched_fragments": 1316, "total_fragments": 2484, "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": 86.0721, "matched_fragments": 1597, "total_fragments": 2484, "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": 85.9824, "matched_fragments": 1600, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum brasilense", "strain": "strain=Sp 7", "accession": "GCA_001315015.1", "taxid": 192, "species_taxid": 192, "relation_to_type": "type", "validated": true, "ani": 85.9402, "matched_fragments": 1532, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum brasilense", "strain": "strain=Sp 7", "accession": "GCA_008274945.1", "taxid": 192, "species_taxid": 192, "relation_to_type": "type", "validated": true, "ani": 85.9318, "matched_fragments": 1586, "total_fragments": 2484, "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": 85.9306, "matched_fragments": 1613, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum brasilense", "strain": "strain=Sp 7", "accession": "GCA_007827425.1", "taxid": 192, "species_taxid": 192, "relation_to_type": "type", "validated": true, "ani": 85.9278, "matched_fragments": 1578, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospirillum brasilense", "strain": "strain=Sp 7", "accession": "GCA_002027385.1", "taxid": 192, "species_taxid": 192, "relation_to_type": "type", "validated": true, "ani": 85.9045, "matched_fragments": 1549, "total_fragments": 2484, "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": 78.1377, "matched_fragments": 751, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nisaea acidiphila", "strain": "strain=MEBiC11861", "accession": "GCA_024662015.1", "taxid": 1862145, "species_taxid": 1862145, "relation_to_type": "type", "validated": true, "ani": 76.8976, "matched_fragments": 254, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovastum atsumiense", "strain": "strain=G2-11", "accession": "GCA_937425535.1", "taxid": 504468, "species_taxid": 504468, "relation_to_type": "type", "validated": true, "ani": 76.5318, "matched_fragments": 535, "total_fragments": 2484, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 8.33, "strain_heterogeneity": 50.0 }, "gtdb_result": [ { "accession": "GCF_017876155.1", "gtdb_species": "s__Azospirillum rugosum", "ani": 99.9965, "matched_fragments": 2474, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "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_003119115.1", "gtdb_species": "s__Azospirillum sp003119115", "ani": 86.3848, "matched_fragments": 1614, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.55", "min_intra_species_ani": "95.10", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_008365405.1", "gtdb_species": "s__Azospirillum brasilense_D", "ani": 86.1496, "matched_fragments": 1551, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "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_008365375.1", "gtdb_species": "s__Azospirillum sp008365375", "ani": 86.1368, "matched_fragments": 1526, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "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_007827815.1", "gtdb_species": "s__Azospirillum brasilense_C", "ani": 86.1118, "matched_fragments": 1593, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.36", "min_intra_species_ani": "95.98", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002245955.1", "gtdb_species": "s__Azospirillum brasilense_A", "ani": 86.0875, "matched_fragments": 1581, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "97.48", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014192915.1", "gtdb_species": "s__Azospirillum sp014192915", "ani": 86.0648, "matched_fragments": 1563, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "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_003119195.2", "gtdb_species": "s__Azospirillum baldaniorum", "ani": 86.0311, "matched_fragments": 1603, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "ani_circumscription_radius": 95.0321, "mean_intra_species_ani": "97.20", "min_intra_species_ani": "95.48", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_003349955.1", "gtdb_species": "s__Azospirillum brasilense_B", "ani": 86.0303, "matched_fragments": 1492, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.36", "min_intra_species_ani": "95.36", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007827795.1", "gtdb_species": "s__Azospirillum brasilense_E", "ani": 85.9864, "matched_fragments": 1530, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001315015.1", "gtdb_species": "s__Azospirillum brasilense", "ani": 85.9508, "matched_fragments": 1530, "total_fragments": 2484, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum", "ani_circumscription_radius": 95.0321, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 16, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.02, "cell_length": 0.408, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 31.365, "optimum_ph": 6.65, "genome_size": 6556262.897, "gc_content": 68.678, "coding_genes": 5382.225, "rRNA16S_genes": 7.916, "tRNA_genes": 82.666, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Azospirillum", "rugosum" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }