{ "type": "genome", "identifier": "GCF_003313505.1", "organism": "Pedobacter nanyangensis", "title": "Pedobacter nanyangensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003313505.1", "bioproject": "PRJNA224116", "biosample": "SAMN09478392", "wgs_master": "QMHO00000000.1", "refseq_category": "reference genome", "taxid": "1562389", "species_taxid": "1562389", "organism_name": "Pedobacter nanyangensis", "infraspecific_name": "strain=Q-4", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/11", "asm_name": "ASM331350v1", "asm_submitter": "Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_003313505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/313/505/GCF_003313505.1_ASM331350v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4736258", "genome_size_ungapped": "4735638", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "25", "contig_count": "25", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003313505.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3962", "protein_coding_gene_count": "3898", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-11", "dateModified": "2018-07-11", "datePublished": "2018-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter nanyangensis" ], "sample_taxid": [ "1562389" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Henan" ], "sample_host_location_id": [], "data_size": "1.341 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)": "4736258", "Number of Sequences": "25", "Longest Sequences (bp)": "724533", "N50 (bp)": "349812", "Gap Ratio (%)": "0.013091", "GCcontent (%)": "41.1", "Number of CDSs": "3870", "Average Protein Length": "358.8", "Coding Ratio (%)": "87.9", "Number of rRNAs": "0", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter nanyangensis", "strain": "strain=Q-4", "accession": "GCA_003313505.1", "taxid": 1562389, "species_taxid": 1562389, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1566, "total_fragments": 1567, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter chitinilyticus", "strain": "strain=CM134L-2", "accession": "GCA_004025525.1", "taxid": 2233776, "species_taxid": 2233776, "relation_to_type": "type", "validated": true, "ani": 84.1023, "matched_fragments": 1095, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter chitinilyticus", "strain": "strain=CM134L-2", "accession": "GCA_003313385.1", "taxid": 2233776, "species_taxid": 2233776, "relation_to_type": "type", "validated": true, "ani": 84.0617, "matched_fragments": 1096, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ureilyticus", "strain": "strain=THG-T11", "accession": "GCA_005925345.1", "taxid": 1393051, "species_taxid": 1393051, "relation_to_type": "type", "validated": true, "ani": 79.9043, "matched_fragments": 609, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter xixiisoli", "strain": "strain=S27", "accession": "GCA_005925365.1", "taxid": 1476464, "species_taxid": 1476464, "relation_to_type": "type", "validated": true, "ani": 79.4904, "matched_fragments": 598, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter xixiisoli", "strain": "strain=CGMCC 1.12803", "accession": "GCA_900215335.1", "taxid": 1476464, "species_taxid": 1476464, "relation_to_type": "type", "validated": true, "ani": 79.4653, "matched_fragments": 599, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter helvus", "strain": "strain=P-25", "accession": "GCA_005925325.1", "taxid": 2563444, "species_taxid": 2563444, "relation_to_type": "type", "validated": true, "ani": 79.3701, "matched_fragments": 595, "total_fragments": 1567, "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": 76.6536, "matched_fragments": 162, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter gilvus", "strain": "strain=F01003", "accession": "GCA_004054195.1", "taxid": 2305909, "species_taxid": 2305909, "relation_to_type": "type", "validated": true, "ani": 76.3989, "matched_fragments": 55, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter achroorhodeus", "strain": "strain=MJ1a", "accession": "GCA_007846095.1", "taxid": 2599294, "species_taxid": 2599294, "relation_to_type": "type", "validated": true, "ani": 76.1037, "matched_fragments": 59, "total_fragments": 1567, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003313505.1", "gtdb_species": "s__Pedobacter nanyangensis", "ani": 100.0, "matched_fragments": 1566, "total_fragments": 1567, "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_003313385.1", "gtdb_species": "s__Pedobacter chitinilyticus", "ani": 84.0617, "matched_fragments": 1096, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "95.89", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005925345.1", "gtdb_species": "s__Pedobacter ureilyticus", "ani": 79.8941, "matched_fragments": 610, "total_fragments": 1567, "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_900215335.1", "gtdb_species": "s__Pedobacter xixiisoli", "ani": 79.4614, "matched_fragments": 599, "total_fragments": 1567, "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_005925325.1", "gtdb_species": "s__Pedobacter helvus", "ani": 79.3619, "matched_fragments": 596, "total_fragments": 1567, "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_003313335.1", "gtdb_species": "s__Pedobacter zeaxanthinifaciens", "ani": 79.2554, "matched_fragments": 538, "total_fragments": 1567, "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_002399615.1", "gtdb_species": "s__Pedobacter sp002399615", "ani": 79.1977, "matched_fragments": 507, "total_fragments": 1567, "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_000633455.1", "gtdb_species": "s__Pedobacter jeongneungensis", "ani": 77.1728, "matched_fragments": 197, "total_fragments": 1567, "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_014200595.1", "gtdb_species": "s__Pedobacter cryoconitis_C", "ani": 76.9604, "matched_fragments": 107, "total_fragments": 1567, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "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", "nanyangensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }