{ "type": "genome", "identifier": "GCF_003349965.1", "organism": "Niabella yanshanensis", "title": "Niabella yanshanensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Helsinki", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003349965.1", "bioproject": "PRJNA224116", "biosample": "SAMN09428663", "wgs_master": "QLKR00000000.1", "refseq_category": "na", "taxid": "577386", "species_taxid": "577386", "organism_name": "Niabella yanshanensis", "infraspecific_name": "strain=HAMBI_3031", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/31", "asm_name": "ASM334996v1", "asm_submitter": "University of Helsinki", "gbrs_paired_asm": "GCA_003349965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/349/965/GCF_003349965.1_ASM334996v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5519621", "genome_size_ungapped": "5519501", "gc_percent": "42.500000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003349965.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4589", "protein_coding_gene_count": "4526", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-31", "dateModified": "2018-07-31", "datePublished": "2018-07-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Niabella yanshanensis" ], "sample_taxid": [ "577386" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.569 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)": "5519621", "Number of Sequences": "25", "Longest Sequences (bp)": "1089344", "N50 (bp)": "633609", "Gap Ratio (%)": "0.002174", "GCcontent (%)": "42.7", "Number of CDSs": "4474", "Average Protein Length": "361.4", "Coding Ratio (%)": "87.9", "Number of rRNAs": "3", "Number of tRNAs": "38", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Niabella yanshanensis", "strain": "strain=HAMBI_3031", "accession": "GCA_003349965.1", "taxid": 577386, "species_taxid": 577386, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1826, "total_fragments": 1828, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Niabella hibiscisoli", "strain": "strain=THG-DN5.5", "accession": "GCA_022512515.1", "taxid": 1825928, "species_taxid": 1825928, "relation_to_type": "type", "validated": true, "ani": 82.0578, "matched_fragments": 1251, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niabella ginsengisoli", "strain": "strain=GR10-1", "accession": "GCA_022513635.1", "taxid": 522298, "species_taxid": 522298, "relation_to_type": "type", "validated": true, "ani": 77.8736, "matched_fragments": 376, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niabella pedocola", "strain": "strain=JCM 31011", "accession": "GCA_021044425.1", "taxid": 1752077, "species_taxid": 1752077, "relation_to_type": "type", "validated": true, "ani": 76.8261, "matched_fragments": 167, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niabella soli", "strain": "strain=JS13-8; DSM 19437", "accession": "GCA_000243115.3", "taxid": 446683, "species_taxid": 446683, "relation_to_type": "type", "validated": true, "ani": 76.7598, "matched_fragments": 132, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niabella ginsenosidivorans", "strain": "strain=BS26", "accession": "GCA_001654455.1", "taxid": 1176587, "species_taxid": 1176587, "relation_to_type": "type", "validated": true, "ani": 76.442, "matched_fragments": 149, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pinibacter aurantiacus", "strain": "strain=MAH-26", "accession": "GCA_019130065.1", "taxid": 2851599, "species_taxid": 2851599, "relation_to_type": "type", "validated": true, "ani": 76.327, "matched_fragments": 65, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niabella beijingensis", "strain": "strain=3A5MI-3", "accession": "GCA_020034665.1", "taxid": 2872700, "species_taxid": 2872700, "relation_to_type": "type", "validated": true, "ani": 76.3209, "matched_fragments": 143, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niastella populi", "strain": "strain=CCTCC AB 208238", "accession": "GCA_002078015.1", "taxid": 550983, "species_taxid": 550983, "relation_to_type": "type", "validated": true, "ani": 76.2657, "matched_fragments": 60, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Filimonas lacunae", "strain": "strain=NBRC 104114", "accession": "GCA_002355595.1", "taxid": 477680, "species_taxid": 477680, "relation_to_type": "type", "validated": true, "ani": 76.2296, "matched_fragments": 67, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Filimonas lacunae", "strain": "strain=DSM 21054", "accession": "GCA_900156765.1", "taxid": 477680, "species_taxid": 477680, "relation_to_type": "type", "validated": true, "ani": 76.2296, "matched_fragments": 67, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paraflavitalea soli", "strain": "strain=5GH32-13", "accession": "GCA_003555545.1", "taxid": 2315862, "species_taxid": 2315862, "relation_to_type": "type", "validated": true, "ani": 75.9988, "matched_fragments": 70, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Filimonas zeae", "strain": "strain=CGMCC 1.15290", "accession": "GCA_014641615.1", "taxid": 1737353, "species_taxid": 1737353, "relation_to_type": "type", "validated": true, "ani": 75.9953, "matched_fragments": 76, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Niastella soli", "strain": "strain=MAH-29", "accession": "GCA_017742245.1", "taxid": 2821487, "species_taxid": 2821487, "relation_to_type": "type", "validated": true, "ani": 75.5123, "matched_fragments": 73, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga arvensicola", "strain": "strain=DSM 3695", "accession": "GCA_900110835.1", "taxid": 29529, "species_taxid": 29529, "relation_to_type": "type", "validated": true, "ani": 75.4997, "matched_fragments": 54, "total_fragments": 1828, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003349965.1", "gtdb_species": "s__Niabella yanshanensis", "ani": 100.0, "matched_fragments": 1826, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella", "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_016719165.1", "gtdb_species": "s__JJ008 sp016719165", "ani": 76.8519, "matched_fragments": 54, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.96", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_014168535.1", "gtdb_species": "s__Lacibacter sp014168535", "ani": 76.8069, "matched_fragments": 69, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter", "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_900101395.1", "gtdb_species": "s__Niabella drilacis", "ani": 76.6445, "matched_fragments": 142, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella", "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_000374125.1", "gtdb_species": "s__Niabella aurantiaca", "ani": 76.4955, "matched_fragments": 149, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella", "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_001896965.1", "gtdb_species": "s__Niabella sp001896965", "ani": 76.4622, "matched_fragments": 73, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella", "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_017744715.1", "gtdb_species": "s__Niabella sp017744715", "ani": 76.4586, "matched_fragments": 159, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella", "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_002355595.1", "gtdb_species": "s__Filimonas lacunae", "ani": 76.4572, "matched_fragments": 67, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas", "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_001654455.1", "gtdb_species": "s__Niabella ginsenosidivorans", "ani": 76.4341, "matched_fragments": 147, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella", "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_001898485.1", "gtdb_species": "s__46-32 sp001898485", "ani": 76.4142, "matched_fragments": 58, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__46-32", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.14", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_016710935.1", "gtdb_species": "s__Ferruginibacter sp016710935", "ani": 76.3373, "matched_fragments": 54, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter", "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_002400415.1", "gtdb_species": "s__JJ008 sp002400415", "ani": 76.2962, "matched_fragments": 68, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008", "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_002078015.1", "gtdb_species": "s__Niastella populi", "ani": 76.2657, "matched_fragments": 60, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella", "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_002337125.1", "gtdb_species": "s__Lacibacter sp002337125", "ani": 76.2377, "matched_fragments": 74, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter", "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_001464625.1", "gtdb_species": "s__JJ008 sp001464625", "ani": 76.2197, "matched_fragments": 55, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008", "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_003075435.1", "gtdb_species": "s__Agriterribacter sp003075435", "ani": 76.1911, "matched_fragments": 71, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Agriterribacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.00", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017744795.1", "gtdb_species": "s__Niabella sp017744795", "ani": 76.0795, "matched_fragments": 136, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niabella", "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_003555545.1", "gtdb_species": "s__Paraflavitalea soli", "ani": 75.974, "matched_fragments": 68, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Paraflavitalea", "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_002352145.1", "gtdb_species": "s__JJ008 sp002352145", "ani": 75.8602, "matched_fragments": 53, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008", "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_902826165.1", "gtdb_species": "s__JJ008 sp902826165", "ani": 75.8354, "matched_fragments": 82, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008", "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_004341975.1", "gtdb_species": "s__Niastella sp004341975", "ani": 75.7044, "matched_fragments": 86, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella", "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_017742245.1", "gtdb_species": "s__Niastella sp017742245", "ani": 75.5123, "matched_fragments": 73, "total_fragments": 1828, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella", "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": -0.302, "cell_length": 0.079, "doubling_h": null, "growth_tmp": 28.5, "optimum_tmp": 29.611, "optimum_ph": 6.666, "genome_size": 5587696.854, "gc_content": 46.1, "coding_genes": 4275.583, "rRNA16S_genes": 2.0, "tRNA_genes": 41.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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": [ "Niabella", "yanshanensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }