{ "type": "genome", "identifier": "GCF_010974945.1", "organism": "Noviherbaspirillum galbum", "title": "Noviherbaspirillum galbum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Seoul Women's University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_010974945.1", "bioproject": "PRJNA224116", "biosample": "SAMN14085713", "wgs_master": "JAAIVB000000000.1", "refseq_category": "reference genome", "taxid": "2709383", "species_taxid": "2709383", "organism_name": "Noviherbaspirillum galbum", "infraspecific_name": "strain=17J57-3", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/23", "asm_name": "ASM1097494v1", "asm_submitter": "Seoul Women's University", "gbrs_paired_asm": "GCA_010974945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/974/945/GCF_010974945.1_ASM1097494v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6117206", "genome_size_ungapped": "6117206", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "96", "contig_count": "96", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_010974945.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "5612", "protein_coding_gene_count": "5488", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-23", "dateModified": "2020-02-23", "datePublished": "2020-02-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Noviherbaspirillum galbum" ], "sample_taxid": [ "2709383" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jeju" ], "sample_host_location_id": [], "data_size": "1.700 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)": "6117206", "Number of Sequences": "96", "Longest Sequences (bp)": "404044", "N50 (bp)": "152396", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.3", "Number of CDSs": "5469", "Average Protein Length": "324.9", "Coding Ratio (%)": "87.1", "Number of rRNAs": "0", "Number of tRNAs": "57", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Noviherbaspirillum galbum", "strain": "strain=17J57-3", "accession": "GCA_010974945.1", "taxid": 2709383, "species_taxid": 2709383, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1993, "total_fragments": 1997, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Noviherbaspirillum aridicola", "strain": "strain=NCCP-691", "accession": "GCA_019656455.1", "taxid": 2849687, "species_taxid": 2849687, "relation_to_type": "type", "validated": true, "ani": 81.4024, "matched_fragments": 732, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum humi", "strain": "strain=U15", "accession": "GCA_900188095.1", "taxid": 1688639, "species_taxid": 1688639, "relation_to_type": "type", "validated": true, "ani": 81.018, "matched_fragments": 744, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum malthae", "strain": "strain=CC-AFH3", "accession": "GCA_015352985.1", "taxid": 1260987, "species_taxid": 1260987, "relation_to_type": "type", "validated": true, "ani": 80.7194, "matched_fragments": 840, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum denitrificans", "strain": "strain=TSA40", "accession": "GCA_002211445.1", "taxid": 1968433, "species_taxid": 1968433, "relation_to_type": "type", "validated": true, "ani": 80.5049, "matched_fragments": 747, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum aerium", "strain": "strain=122213-3", "accession": "GCA_008929045.1", "taxid": 2588497, "species_taxid": 2588497, "relation_to_type": "type", "validated": true, "ani": 80.4826, "matched_fragments": 791, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum robiniae", "strain": "strain=HZ10", "accession": "GCA_002213415.1", "taxid": 2014887, "species_taxid": 2014887, "relation_to_type": "type", "validated": true, "ani": 80.1392, "matched_fragments": 607, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum seropedicae", "strain": "strain=Z67", "accession": "GCA_001040945.1", "taxid": 964, "species_taxid": 964, "relation_to_type": "type", "validated": true, "ani": 79.7376, "matched_fragments": 523, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum seropedicae", "strain": "strain=Z67", "accession": "GCA_013180375.1", "taxid": 964, "species_taxid": 964, "relation_to_type": "type", "validated": true, "ani": 79.6539, "matched_fragments": 515, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum camelliae", "strain": "strain=WT00C", "accession": "GCA_001929405.1", "taxid": 1892903, "species_taxid": 1892903, "relation_to_type": "type", "validated": true, "ani": 79.5497, "matched_fragments": 530, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum lusitanum", "strain": "strain=P6-12", "accession": "GCA_000256565.1", "taxid": 213312, "species_taxid": 213312, "relation_to_type": "type", "validated": true, "ani": 79.5294, "matched_fragments": 452, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum cavernae", "strain": "strain=K2R10-39", "accession": "GCA_003590875.1", "taxid": 2320862, "species_taxid": 2320862, "relation_to_type": "type", "validated": true, "ani": 79.487, "matched_fragments": 563, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Herbaspirillum huttiense subsp. putei", "strain": "strain=IAM 15032", "accession": "GCA_000478365.1", "taxid": 230311, "species_taxid": 863372, "relation_to_type": "type", "validated": true, "ani": 79.3376, "matched_fragments": 529, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Collimonas humicola", "strain": "strain=RLT1W51", "accession": "GCA_018304945.1", "taxid": 2825886, "species_taxid": 2825886, "relation_to_type": "type", "validated": true, "ani": 79.2336, "matched_fragments": 453, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Massilia agri", "strain": "strain=JCM 31661", "accession": "GCA_024753255.1", "taxid": 1886785, "species_taxid": 1886785, "relation_to_type": "type", "validated": true, "ani": 79.1863, "matched_fragments": 581, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Noviherbaspirillum saxi", "strain": "strain=K1R23-30", "accession": "GCA_003591035.1", "taxid": 2320863, "species_taxid": 2320863, "relation_to_type": "type", "validated": true, "ani": 79.0987, "matched_fragments": 604, "total_fragments": 1997, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010974945.1", "gtdb_species": "s__Noviherbaspirillum galbum", "ani": 100.0, "matched_fragments": 1993, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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": "GCA_004570315.1", "gtdb_species": "s__Noviherbaspirillum sp004570315", "ani": 81.0984, "matched_fragments": 692, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_900188095.1", "gtdb_species": "s__Noviherbaspirillum humi", "ani": 81.0149, "matched_fragments": 743, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_015352985.1", "gtdb_species": "s__Noviherbaspirillum malthae", "ani": 80.6873, "matched_fragments": 843, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_007874125.1", "gtdb_species": "s__Noviherbaspirillum sp007874125", "ani": 80.5618, "matched_fragments": 716, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_002211445.1", "gtdb_species": "s__Noviherbaspirillum denitrificans", "ani": 80.5092, "matched_fragments": 746, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_008929045.1", "gtdb_species": "s__Noviherbaspirillum aerium", "ani": 80.4904, "matched_fragments": 790, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_017744395.1", "gtdb_species": "s__Herbaspirillum sp017744395", "ani": 80.4127, "matched_fragments": 559, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "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_002213415.1", "gtdb_species": "s__Herbaspirillum robiniae", "ani": 80.1389, "matched_fragments": 607, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.55", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_017814915.1", "gtdb_species": "s__Herbaspirillum sp017814915", "ani": 80.1196, "matched_fragments": 562, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "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_006715495.1", "gtdb_species": "s__Herbaspirillum sp006715495", "ani": 80.1143, "matched_fragments": 536, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.71", "min_intra_species_ani": "99.15", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_009914615.1", "gtdb_species": "s__Herbaspirillum frisingense_B", "ani": 80.0952, "matched_fragments": 506, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "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_000818395.1", "gtdb_species": "s__Noviherbaspirillum autotrophicum", "ani": 79.982, "matched_fragments": 649, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_015352955.1", "gtdb_species": "s__Noviherbaspirillum_A soli", "ani": 79.9808, "matched_fragments": 665, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A", "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_001040945.1", "gtdb_species": "s__Herbaspirillum seropedicae", "ani": 79.7387, "matched_fragments": 522, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "96.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_003590875.1", "gtdb_species": "s__Noviherbaspirillum sp003590875", "ani": 79.5184, "matched_fragments": 558, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum", "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_003537575.1", "gtdb_species": "s__Paucimonas sp003537575", "ani": 79.4874, "matched_fragments": 471, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas", "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_004367745.1", "gtdb_species": "s__Herbaspirillum huttiense", "ani": 79.3698, "matched_fragments": 530, "total_fragments": 1997, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.45", "min_intra_species_ani": "97.06", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 14, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.035, "cell_length": 0.311, "doubling_h": null, "growth_tmp": 28.2, "optimum_tmp": 26.2, "optimum_ph": 6.75, "genome_size": 5334859.666, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.166, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.833, "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": [ "Noviherbaspirillum", "galbum" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }