{ "type": "genome", "identifier": "GCF_900111825.1", "organism": "Pedobacter suwonensis", "title": "Pedobacter suwonensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900111825.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488511", "wgs_master": "FOJM00000000.1", "refseq_category": "na", "taxid": "332999", "species_taxid": "332999", "organism_name": "Pedobacter suwonensis", "infraspecific_name": "strain=DSM 18130", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/04", "asm_name": "IMG-taxon 2622736524 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900111825.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/111/825/GCF_900111825.1_IMG-taxon_2622736524_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5803831", "genome_size_ungapped": "5801156", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "40", "contig_count": "40", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900111825.1-RS_2024_11_06", "annotation_date": "2024-11-06", "total_gene_count": "4820", "protein_coding_gene_count": "4742", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-04", "dateModified": "2016-11-04", "datePublished": "2016-11-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter suwonensis" ], "sample_taxid": [ "332999" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.641 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5803831", "Number of Sequences": "40", "Longest Sequences (bp)": "627276", "N50 (bp)": "260382", "Gap Ratio (%)": "0.046090", "GCcontent (%)": "39.5", "Number of CDSs": "4701", "Average Protein Length": "343.9", "Coding Ratio (%)": "83.6", "Number of rRNAs": "1", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter suwonensis", "strain": "strain=DSM 18130", "accession": "GCA_900111825.1", "taxid": 332999, "species_taxid": 332999, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1911, "total_fragments": 1914, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter terrae", "strain": "strain=DSM 17933", "accession": "GCA_900100705.1", "taxid": 405671, "species_taxid": 405671, "relation_to_type": "type", "validated": true, "ani": 86.551, "matched_fragments": 1338, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_004402005.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 83.863, "matched_fragments": 1214, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_003664035.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 83.8473, "matched_fragments": 1230, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter borealis", "strain": "strain=DSM 19626", "accession": "GCA_000708285.2", "taxid": 475254, "species_taxid": 475254, "relation_to_type": "type", "validated": true, "ani": 83.1965, "matched_fragments": 986, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ginsenosidimutans", "strain": "strain=KACC 14530", "accession": "GCA_001442625.1", "taxid": 687842, "species_taxid": 687842, "relation_to_type": "type", "validated": true, "ani": 82.7571, "matched_fragments": 1147, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter kyonggii", "strain": "strain=K-4-11-1", "accession": "GCA_004310665.1", "taxid": 1926871, "species_taxid": 1926871, "relation_to_type": "type", "validated": true, "ani": 82.7389, "matched_fragments": 1127, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrodurus", "strain": "strain=RP-3-21", "accession": "GCA_004331735.1", "taxid": 2530456, "species_taxid": 2530456, "relation_to_type": "type", "validated": true, "ani": 82.6994, "matched_fragments": 1093, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter zeae", "strain": "strain=DSM 100774", "accession": "GCA_014196715.1", "taxid": 1737356, "species_taxid": 1737356, "relation_to_type": "type", "validated": true, "ani": 82.0614, "matched_fragments": 1056, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter zeae", "strain": "strain=CGMCC 1.15287", "accession": "GCA_014641575.1", "taxid": 1737356, "species_taxid": 1737356, "relation_to_type": "type", "validated": true, "ani": 82.0514, "matched_fragments": 1072, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter kyungheensis", "strain": "strain=KACC 16221", "accession": "GCA_000812965.1", "taxid": 1069985, "species_taxid": 1069985, "relation_to_type": "type", "validated": true, "ani": 81.4008, "matched_fragments": 927, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter soli", "strain": "strain=DSM 18609", "accession": "GCA_900101435.1", "taxid": 390242, "species_taxid": 390242, "relation_to_type": "type", "validated": true, "ani": 81.3881, "matched_fragments": 949, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ghigonis", "strain": "strain=Marseille-Q2390", "accession": "GCA_903166585.1", "taxid": 2730403, "species_taxid": 2730403, "relation_to_type": "type", "validated": true, "ani": 81.2645, "matched_fragments": 896, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter fastidiosus", "strain": "strain=CCM 8938", "accession": "GCA_014306625.1", "taxid": 2765361, "species_taxid": 2765361, "relation_to_type": "type", "validated": true, "ani": 79.2747, "matched_fragments": 655, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter agri", "strain": "strain=R11", "accession": "GCA_009928685.1", "taxid": 2695265, "species_taxid": 2695265, "relation_to_type": "type", "validated": true, "ani": 76.7873, "matched_fragments": 92, "total_fragments": 1914, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900111825.1", "gtdb_species": "s__Pedobacter suwonensis", "ani": 100.0, "matched_fragments": 1911, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.36", "min_intra_species_ani": "97.36", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_900100705.1", "gtdb_species": "s__Pedobacter terrae", "ani": 86.5533, "matched_fragments": 1336, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_016909215.1", "gtdb_species": "s__Pedobacter terrae_B", "ani": 85.5263, "matched_fragments": 1312, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_007994015.1", "gtdb_species": "s__Pedobacter terrae_A", "ani": 84.2992, "matched_fragments": 1306, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_005938645.2", "gtdb_species": "s__Pedobacter sp005938645", "ani": 83.8865, "matched_fragments": 1324, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_003664035.1", "gtdb_species": "s__Pedobacter alluvionis", "ani": 83.8584, "matched_fragments": 1228, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_004342125.1", "gtdb_species": "s__Pedobacter sp004342125", "ani": 83.7723, "matched_fragments": 1228, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.29", "min_intra_species_ani": "95.29", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014205835.1", "gtdb_species": "s__Pedobacter sp014205835", "ani": 83.4585, "matched_fragments": 1145, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_014692875.1", "gtdb_species": "s__Pedobacter sp011759615", "ani": 83.27, "matched_fragments": 1141, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_002151545.1", "gtdb_species": "s__Pedobacter sp002151545", "ani": 82.6575, "matched_fragments": 1118, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_017745075.1", "gtdb_species": "s__Pedobacter sp017745075", "ani": 82.2672, "matched_fragments": 1089, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_000812965.1", "gtdb_species": "s__Pedobacter kyungheensis", "ani": 81.4317, "matched_fragments": 922, "total_fragments": 1914, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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": -0.188, "cell_length": 0.361, "doubling_h": null, "growth_tmp": 30.0, "optimum_tmp": 34.0, "optimum_ph": 6.75, "genome_size": 5803831.0, "gc_content": 42.651, "coding_genes": 4725.333, "rRNA16S_genes": 4.333, "tRNA_genes": 57.25, "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": 0.5, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.5, "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": [ "Pedobacter", "suwonensis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }