{ "type": "genome", "identifier": "GCF_003339865.1", "organism": "Pedobacter chinensis", "title": "Pedobacter chinensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "shandong university", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003339865.1", "bioproject": "PRJNA224116", "biosample": "SAMN09685244", "wgs_master": "QPKV00000000.1", "refseq_category": "reference genome", "taxid": "2282421", "species_taxid": "2282421", "organism_name": "Pedobacter chinensis", "infraspecific_name": "strain=JDX94", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/25", "asm_name": "ASM333986v1", "asm_submitter": "shandong university", "gbrs_paired_asm": "GCA_003339865.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/339/865/GCF_003339865.1_ASM333986v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5448160", "genome_size_ungapped": "5448160", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "24", "contig_count": "24", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003339865.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4652", "protein_coding_gene_count": "4576", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-25", "dateModified": "2018-07-25", "datePublished": "2018-07-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter chinensis" ], "sample_taxid": [ "2282421" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Weihai" ], "sample_host_location_id": [], "data_size": "1.524 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)": "5448160", "Number of Sequences": "24", "Longest Sequences (bp)": "1154839", "N50 (bp)": "720476", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "37.5", "Number of CDSs": "4562", "Average Protein Length": "336.1", "Coding Ratio (%)": "84.4", "Number of rRNAs": "5", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter chinensis", "strain": "strain=JDX94", "accession": "GCA_003339865.1", "taxid": 2282421, "species_taxid": 2282421, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1800, "total_fragments": 1803, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter agri", "strain": "strain=PB92", "accession": "GCA_000258495.1", "taxid": 454586, "species_taxid": 454586, "relation_to_type": "type", "validated": true, "ani": 80.8113, "matched_fragments": 747, "total_fragments": 1803, "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": 80.7985, "matched_fragments": 789, "total_fragments": 1803, "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": 80.6151, "matched_fragments": 756, "total_fragments": 1803, "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": 80.6083, "matched_fragments": 707, "total_fragments": 1803, "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": 80.6028, "matched_fragments": 751, "total_fragments": 1803, "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": 80.5829, "matched_fragments": 758, "total_fragments": 1803, "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": 80.4854, "matched_fragments": 730, "total_fragments": 1803, "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": 80.2068, "matched_fragments": 700, "total_fragments": 1803, "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": 80.2043, "matched_fragments": 658, "total_fragments": 1803, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter terrae", "strain": "strain=DSM 17933", "accession": "GCA_900100705.1", "taxid": 405671, "species_taxid": 405671, "relation_to_type": "type", "validated": true, "ani": 80.1924, "matched_fragments": 679, "total_fragments": 1803, "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": 80.1478, "matched_fragments": 742, "total_fragments": 1803, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter miscanthi", "strain": "strain=RS10", "accession": "GCA_003315595.1", "taxid": 2259170, "species_taxid": 2259170, "relation_to_type": "type", "validated": true, "ani": 80.1424, "matched_fragments": 738, "total_fragments": 1803, "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": 80.1145, "matched_fragments": 702, "total_fragments": 1803, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter aquae", "strain": "strain=CJ43", "accession": "GCA_008195825.1", "taxid": 2605747, "species_taxid": 2605747, "relation_to_type": "type", "validated": true, "ani": 76.6235, "matched_fragments": 119, "total_fragments": 1803, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003339865.1", "gtdb_species": "s__Pedobacter chinensis", "ani": 100.0, "matched_fragments": 1800, "total_fragments": 1803, "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_014395225.1", "gtdb_species": "s__Pedobacter roseus", "ani": 80.9185, "matched_fragments": 776, "total_fragments": 1803, "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": 80.816, "matched_fragments": 787, "total_fragments": 1803, "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_000258495.1", "gtdb_species": "s__Pedobacter agri", "ani": 80.8006, "matched_fragments": 748, "total_fragments": 1803, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "97.42", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003173575.1", "gtdb_species": "s__Pedobacter paludis", "ani": 80.7453, "matched_fragments": 757, "total_fragments": 1803, "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_001442625.1", "gtdb_species": "s__Pedobacter ginsenosidimutans", "ani": 80.6265, "matched_fragments": 755, "total_fragments": 1803, "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_004331735.1", "gtdb_species": "s__Pedobacter sp004331735", "ani": 80.5983, "matched_fragments": 752, "total_fragments": 1803, "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_001422545.1", "gtdb_species": "s__Pedobacter sp001422545", "ani": 80.5929, "matched_fragments": 784, "total_fragments": 1803, "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": 80.5867, "matched_fragments": 710, "total_fragments": 1803, "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": 80.5625, "matched_fragments": 761, "total_fragments": 1803, "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_002151545.1", "gtdb_species": "s__Pedobacter sp002151545", "ani": 80.5541, "matched_fragments": 771, "total_fragments": 1803, "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_003387415.1", "gtdb_species": "s__Pedobacter sp003387415", "ani": 80.5533, "matched_fragments": 740, "total_fragments": 1803, "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": 80.495, "matched_fragments": 572, "total_fragments": 1803, "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": 80.4914, "matched_fragments": 747, "total_fragments": 1803, "gtdb_taxonomy": 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"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", "chinensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }