{ "type": "genome", "identifier": "GCF_003173595.1", "organism": "Pedobacter yonginense", "title": "Pedobacter yonginense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Huazhong Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003173595.1", "bioproject": "PRJNA224116", "biosample": "SAMN09095723", "wgs_master": "QGNZ00000000.1", "refseq_category": "reference genome", "taxid": "651869", "species_taxid": "651869", "organism_name": "Pedobacter yonginense", "infraspecific_name": "strain=KCTC22721", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/28", "asm_name": "ASM317359v1", "asm_submitter": "Huazhong Agricultural University", "gbrs_paired_asm": "GCA_003173595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/173/595/GCF_003173595.1_ASM317359v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4372417", "genome_size_ungapped": "4372417", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "15", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003173595.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3767", "protein_coding_gene_count": "3703", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-28", "dateModified": "2018-05-28", "datePublished": "2018-05-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter yonginense" ], "sample_taxid": [ "651869" ], "sample_host_organism": [ "lake" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea:artificial lake" ], "sample_host_location_id": [], "data_size": "1.227 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)": "4372417", "Number of Sequences": "15", "Longest Sequences (bp)": "1564723", "N50 (bp)": "1108272", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.0", "Number of CDSs": "3692", "Average Protein Length": "339.5", "Coding Ratio (%)": "86.0", "Number of rRNAs": "4", "Number of tRNAs": "45", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter yonginense", "strain": "strain=KCTC22721", "accession": "GCA_003173595.1", "taxid": 651869, "species_taxid": 651869, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1452, "total_fragments": 1453, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter fastidiosus", "strain": "strain=CCM 8938", "accession": "GCA_014306625.1", "taxid": 2765361, "species_taxid": 2765361, "relation_to_type": "type", "validated": true, "ani": 82.4992, "matched_fragments": 949, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter frigidisoli", "strain": "strain=RP-3-11", "accession": "GCA_004331675.1", "taxid": 2530455, "species_taxid": 2530455, "relation_to_type": "type", "validated": true, "ani": 80.4639, "matched_fragments": 637, "total_fragments": 1453, "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": 80.1774, "matched_fragments": 604, "total_fragments": 1453, "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": 80.1421, "matched_fragments": 617, "total_fragments": 1453, "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": 80.0866, "matched_fragments": 613, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter chinensis", "strain": "strain=JDX94", "accession": "GCA_003339865.1", "taxid": 2282421, "species_taxid": 2282421, "relation_to_type": "type", "validated": true, "ani": 80.0762, "matched_fragments": 597, "total_fragments": 1453, "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": 80.0327, "matched_fragments": 638, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter nototheniae", "strain": "strain=36B243", "accession": "GCA_004335085.1", "taxid": 2488994, "species_taxid": 2488994, "relation_to_type": "type", "validated": true, "ani": 79.9695, "matched_fragments": 561, "total_fragments": 1453, "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": 79.9091, "matched_fragments": 600, "total_fragments": 1453, "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": 79.8501, "matched_fragments": 605, "total_fragments": 1453, "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": 79.7629, "matched_fragments": 582, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter mucosus", "strain": "strain=Q8-18", "accession": "GCA_022200785.1", "taxid": 2895286, "species_taxid": 2895286, "relation_to_type": "type", "validated": true, "ani": 79.6274, "matched_fragments": 578, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrotolerans", "strain": "strain=DSM 103236", "accession": "GCA_004340665.1", "taxid": 1843235, "species_taxid": 1843235, "relation_to_type": "type", "validated": true, "ani": 79.4792, "matched_fragments": 539, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrotolerans", "strain": "strain=CGMCC 1.15644", "accession": "GCA_014643495.1", "taxid": 1843235, "species_taxid": 1843235, "relation_to_type": "type", "validated": true, "ani": 79.4299, "matched_fragments": 534, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter changchengzhani", "strain": "strain=E01020", "accession": "GCA_004354365.1", "taxid": 2529274, "species_taxid": 2529274, "relation_to_type": "type", "validated": true, "ani": 78.9306, "matched_fragments": 399, "total_fragments": 1453, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003173595.1", "gtdb_species": "s__Pedobacter yonginense", "ani": 100.0, "matched_fragments": 1452, "total_fragments": 1453, "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": "conclusive" }, { "accession": "GCF_003173575.1", "gtdb_species": "s__Pedobacter paludis", "ani": 82.5713, "matched_fragments": 940, "total_fragments": 1453, "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_014306625.1", "gtdb_species": "s__Pedobacter sp014306625", "ani": 82.4935, "matched_fragments": 950, "total_fragments": 1453, "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_004331675.1", "gtdb_species": "s__Pedobacter sp004331675", "ani": 80.4753, "matched_fragments": 636, "total_fragments": 1453, "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_000708285.2", "gtdb_species": "s__Pedobacter borealis", "ani": 80.1681, "matched_fragments": 605, "total_fragments": 1453, "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_004310665.1", "gtdb_species": "s__Pedobacter kyonggii", "ani": 80.0676, "matched_fragments": 615, "total_fragments": 1453, "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_018613605.1", "gtdb_species": "s__Pedobacter sp018613605", "ani": 80.0504, "matched_fragments": 618, "total_fragments": 1453, "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": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004335085.1", "gtdb_species": "s__Pedobacter nototheniae", "ani": 79.9716, "matched_fragments": 560, "total_fragments": 1453, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "98.28", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014635725.1", "gtdb_species": "s__Pedobacter mendelii", "ani": 79.9281, "matched_fragments": 610, "total_fragments": 1453, "gtdb_taxonomy": 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"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_003725795.1", "gtdb_species": "s__Pedobacter jejuensis", "ani": 79.6657, "matched_fragments": 621, "total_fragments": 1453, "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_004210715.1", "gtdb_species": "s__Pedobacter sp004210715", "ani": 79.2979, "matched_fragments": 396, "total_fragments": 1453, "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": -0.28, "cell_length": 0.284, "doubling_h": null, "growth_tmp": 24.703, "optimum_tmp": 25.616, "optimum_ph": 7.026, "genome_size": 5519163.389, "gc_content": 42.651, "coding_genes": 4725.333, "rRNA16S_genes": 4.333, "tRNA_genes": 57.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.281, "range_salinity": null, "facultative_respiration": 0.031, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.968, "mesophilic_range_tmp": 0.5, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.5, "bacillus_cell_shape": 0.939, "coccus_cell_shape": 0.06, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "yonginense" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }