{ "type": "genome", "identifier": "GCF_003208655.1", "organism": "Pedobacter nutrimenti", "title": "Pedobacter nutrimenti", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003208655.1", "bioproject": "PRJNA224116", "biosample": "SAMN06297424", "wgs_master": "QKLU00000000.1", "refseq_category": "reference genome", "taxid": "1241337", "species_taxid": "1241337", "organism_name": "Pedobacter nutrimenti", "infraspecific_name": "strain=DSM 27372", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/12", "asm_name": "ASM320865v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003208655.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/208/655/GCF_003208655.1_ASM320865v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5716991", "genome_size_ungapped": "5715103", "gc_percent": "41.500000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "21", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003208655.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4929", "protein_coding_gene_count": "4862", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-12", "dateModified": "2018-06-12", "datePublished": "2018-06-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter nutrimenti" ], "sample_taxid": [ "1241337" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.612 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)": "5716991", "Number of Sequences": "21", "Longest Sequences (bp)": "1091839", "N50 (bp)": "757267", "Gap Ratio (%)": "0.033024", "GCcontent (%)": "41.6", "Number of CDSs": "4833", "Average Protein Length": "355.8", "Coding Ratio (%)": "90.2", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter nutrimenti", "strain": "strain=DSM 27372", "accession": "GCA_003208655.1", "taxid": 1241337, "species_taxid": 1241337, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1894, "total_fragments": 1894, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter caeni", "strain": "strain=DSM 16990", "accession": "GCA_900129215.1", "taxid": 288992, "species_taxid": 288992, "relation_to_type": "type", "validated": true, "ani": 78.9613, "matched_fragments": 378, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter frigoris", "strain": "strain=RP-3-15", "accession": "GCA_005116445.1", "taxid": 2571272, "species_taxid": 2571272, "relation_to_type": "type", "validated": true, "ani": 78.8054, "matched_fragments": 248, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter duraquae", "strain": "strain=DSM 19034", "accession": "GCA_004362245.1", "taxid": 425511, "species_taxid": 425511, "relation_to_type": "type", "validated": true, "ani": 78.3204, "matched_fragments": 226, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter heparinus", "strain": "strain=DSM 2366", "accession": "GCA_000023825.1", "taxid": 984, "species_taxid": 984, "relation_to_type": "type", "validated": true, "ani": 78.1077, "matched_fragments": 321, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter lusitanus", "strain": "strain=NL19", "accession": "GCA_000832545.1", "taxid": 1503925, "species_taxid": 1503925, "relation_to_type": "type", "validated": true, "ani": 78.0077, "matched_fragments": 265, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter schmidteae", "strain": "strain=eg", "accession": "GCA_900564155.1", "taxid": 2201271, "species_taxid": 2201271, "relation_to_type": "type", "validated": true, "ani": 77.9662, "matched_fragments": 300, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter westerhofensis", "strain": "strain=DSM 19036", "accession": "GCA_900182595.1", "taxid": 425512, "species_taxid": 425512, "relation_to_type": "type", "validated": true, "ani": 77.9625, "matched_fragments": 251, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter antarcticus", "strain": "strain=ATCC 51969", "accession": "GCA_900112985.1", "taxid": 34086, "species_taxid": 34086, "relation_to_type": "type", "validated": true, "ani": 77.8858, "matched_fragments": 213, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter antarcticus", "strain": "strain=4BY", "accession": "GCA_000722885.1", "taxid": 34086, "species_taxid": 34086, "relation_to_type": "type", "validated": true, "ani": 77.8761, "matched_fragments": 209, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter hiemivivus", "strain": "strain=RP-3-8", "accession": "GCA_004331685.1", "taxid": 2530454, "species_taxid": 2530454, "relation_to_type": "type", "validated": true, "ani": 77.7792, "matched_fragments": 272, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter gandavensis", "strain": "strain=LMG 31462", "accession": "GCA_014172405.1", "taxid": 2679963, "species_taxid": 2679963, "relation_to_type": "type", "validated": true, "ani": 77.6547, "matched_fragments": 289, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter steynii", "strain": "strain=DSM 19110", "accession": "GCA_900103665.1", "taxid": 430522, "species_taxid": 430522, "relation_to_type": "type", "validated": true, "ani": 77.6103, "matched_fragments": 355, "total_fragments": 1894, "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": 77.1303, "matched_fragments": 143, "total_fragments": 1894, "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": 76.9591, "matched_fragments": 173, "total_fragments": 1894, "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": 76.0974, "matched_fragments": 51, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter phyllosphaerae", "strain": "strain=PP-F2FG21", "accession": "GCA_004378255.1", "taxid": 1812349, "species_taxid": 1812349, "relation_to_type": "type", "validated": true, "ani": 76.0956, "matched_fragments": 57, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter conchicola", "strain": "strain=MYSH2", "accession": "GCA_003432115.1", "taxid": 2303333, "species_taxid": 2303333, "relation_to_type": "type", "validated": true, "ani": 75.8277, "matched_fragments": 68, "total_fragments": 1894, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003208655.1", "gtdb_species": "s__Pedobacter nutrimenti", "ani": 100.0, "matched_fragments": 1894, "total_fragments": 1894, "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_004364225.1", "gtdb_species": "s__Pedobacter sp004364225", "ani": 79.4833, "matched_fragments": 586, "total_fragments": 1894, "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_001590605.1", "gtdb_species": "s__Pedobacter cryoconitis_A", "ani": 79.1873, "matched_fragments": 288, "total_fragments": 1894, "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_003061025.1", "gtdb_species": "s__Pedobacter sp003061025", "ani": 79.102, "matched_fragments": 506, "total_fragments": 1894, "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_900129215.1", "gtdb_species": "s__Pedobacter caeni", "ani": 78.9548, "matched_fragments": 378, "total_fragments": 1894, "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_015752175.1", "gtdb_species": "s__Pedobacter sp015752175", "ani": 78.8064, "matched_fragments": 288, "total_fragments": 1894, "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_005116445.1", "gtdb_species": "s__Pedobacter sp005116445", "ani": 78.8054, "matched_fragments": 248, "total_fragments": 1894, "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_002736205.1", "gtdb_species": "s__Pedobacter ginsengisoli", "ani": 78.3043, "matched_fragments": 258, "total_fragments": 1894, "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_004362245.1", "gtdb_species": "s__Pedobacter duraquae", "ani": 78.3032, "matched_fragments": 227, "total_fragments": 1894, "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_015223055.1", "gtdb_species": "s__Pedobacter sp015223055", "ani": 78.0666, "matched_fragments": 293, "total_fragments": 1894, "gtdb_taxonomy": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "nutrimenti" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }