{ "type": "genome", "identifier": "GCF_014172405.1", "organism": "Pedobacter gandavensis", "title": "Pedobacter gandavensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ghent University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014172405.1", "bioproject": "PRJNA224116", "biosample": "SAMN13388993", "wgs_master": "WNXC00000000.1", "refseq_category": "reference genome", "taxid": "2679963", "species_taxid": "2679963", "organism_name": "Pedobacter gandavensis", "infraspecific_name": "strain=LMG 31462", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/12", "asm_name": "ASM1417240v1", "asm_submitter": "Ghent University", "gbrs_paired_asm": "GCA_014172405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/172/405/GCF_014172405.1_ASM1417240v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5585794", "genome_size_ungapped": "5585794", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "21", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014172405.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4735", "protein_coding_gene_count": "4649", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-12", "dateModified": "2020-08-12", "datePublished": "2020-08-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter gandavensis" ], "sample_taxid": [ "2679963" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Belgium:Ghent" ], "sample_host_location_id": [], "data_size": "1.582 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)": "5585794", "Number of Sequences": "21", "Longest Sequences (bp)": "1919339", "N50 (bp)": "477541", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.8", "Number of CDSs": "4625", "Average Protein Length": "361.2", "Coding Ratio (%)": "89.7", "Number of rRNAs": "1", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter gandavensis", "strain": "strain=LMG 31462", "accession": "GCA_014172405.1", "taxid": 2679963, "species_taxid": 2679963, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1850, "total_fragments": 1851, "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": 81.1396, "matched_fragments": 769, "total_fragments": 1851, "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": 80.9989, "matched_fragments": 783, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter nyackensis", "strain": "strain=DSM 19625", "accession": "GCA_900176505.1", "taxid": 475255, "species_taxid": 475255, "relation_to_type": "type", "validated": true, "ani": 79.0403, "matched_fragments": 421, "total_fragments": 1851, "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": 78.9911, "matched_fragments": 427, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter foliorum", "strain": "strain=LMG 31463", "accession": "GCA_013266735.1", "taxid": 2739058, "species_taxid": 2739058, "relation_to_type": "type", "validated": true, "ani": 78.8633, "matched_fragments": 406, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter panaciterrae", "strain": "strain=LMG 23400", "accession": "GCA_013204795.1", "taxid": 363849, "species_taxid": 363849, "relation_to_type": "type", "validated": true, "ani": 78.7277, "matched_fragments": 370, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter metabolipauper", "strain": "strain=DSM 19035", "accession": "GCA_004362715.1", "taxid": 425513, "species_taxid": 425513, "relation_to_type": "type", "validated": true, "ani": 78.4845, "matched_fragments": 342, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter polaris", "strain": "strain=RP-3-22", "accession": "GCA_005116505.1", "taxid": 2571273, "species_taxid": 2571273, "relation_to_type": "type", "validated": true, "ani": 78.2589, "matched_fragments": 185, "total_fragments": 1851, "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": 78.1349, "matched_fragments": 295, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter namyangjuensis", "strain": "strain=5G38", "accession": "GCA_003313325.1", "taxid": 600626, "species_taxid": 600626, "relation_to_type": "type", "validated": true, "ani": 77.9673, "matched_fragments": 160, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter planticolens", "strain": "strain=LMG 31464", "accession": "GCA_014172375.1", "taxid": 2679964, "species_taxid": 2679964, "relation_to_type": "type", "validated": true, "ani": 77.9243, "matched_fragments": 198, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter nutrimenti", "strain": "strain=DSM 27372", "accession": "GCA_003208655.1", "taxid": 1241337, "species_taxid": 1241337, "relation_to_type": "type", "validated": true, "ani": 77.8132, "matched_fragments": 284, "total_fragments": 1851, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014172405.1", "gtdb_species": "s__Pedobacter gandavensis", 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1259, "total_fragments": 1851, "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": 81.1514, "matched_fragments": 767, "total_fragments": 1851, "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_900103665.1", "gtdb_species": "s__Pedobacter steynii", "ani": 81.0134, "matched_fragments": 780, "total_fragments": 1851, "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_003852525.1", "gtdb_species": "s__Pedobacter sp003852525", "ani": 80.9819, "matched_fragments": 794, "total_fragments": 1851, "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_003208655.1", "gtdb_species": "s__Pedobacter nutrimenti", "ani": 77.8457, "matched_fragments": 283, "total_fragments": 1851, "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", "gandavensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }