{ "type": "genome", "identifier": "GCF_013204795.1", "organism": "Pedobacter panaciterrae", "title": "Pedobacter panaciterrae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Ghent University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013204795.1", "bioproject": "PRJNA224116", "biosample": "SAMN15015933", "wgs_master": "JABMKW000000000.1", "refseq_category": "reference genome", "taxid": "363849", "species_taxid": "363849", "organism_name": "Pedobacter panaciterrae", "infraspecific_name": "strain=LMG 23400", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/01", "asm_name": "ASM1320479v1", "asm_submitter": "Ghent University", "gbrs_paired_asm": "GCA_013204795.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/204/795/GCF_013204795.1_ASM1320479v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6228419", "genome_size_ungapped": "6228419", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013204795.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "5352", "protein_coding_gene_count": "5290", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-01", "dateModified": "2020-06-01", "datePublished": "2020-06-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter panaciterrae" ], "sample_taxid": [ "363849" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea:Pocheon" ], "sample_host_location_id": [], "data_size": "1.766 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)": "6228419", "Number of Sequences": "20", "Longest Sequences (bp)": "1807708", "N50 (bp)": "982404", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.7", "Number of CDSs": "5222", "Average Protein Length": "357.8", "Coding Ratio (%)": "90.0", "Number of rRNAs": "1", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter panaciterrae", "strain": "strain=LMG 23400", "accession": "GCA_013204795.1", "taxid": 363849, "species_taxid": 363849, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2065, "total_fragments": 2066, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter foliorum", "strain": "strain=LMG 31463", "accession": "GCA_013266735.1", "taxid": 2739058, "species_taxid": 2739058, "relation_to_type": "type", "validated": true, "ani": 84.2813, "matched_fragments": 1292, "total_fragments": 2066, "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": 79.4119, "matched_fragments": 460, "total_fragments": 2066, "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": 79.1689, "matched_fragments": 477, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter heparinus", "strain": "strain=DSM 2366", "accession": "GCA_000410815.1", "taxid": 984, "species_taxid": 984, "relation_to_type": "type", "validated": true, "ani": 79.055, "matched_fragments": 425, "total_fragments": 2066, "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": 79.0104, "matched_fragments": 424, "total_fragments": 2066, "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": 78.9928, "matched_fragments": 414, "total_fragments": 2066, "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": 78.9301, "matched_fragments": 486, "total_fragments": 2066, "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": 78.762, "matched_fragments": 382, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter caeni", "strain": "strain=DSM 16990", "accession": "GCA_900129215.1", "taxid": 288992, "species_taxid": 288992, "relation_to_type": "type", "validated": true, "ani": 78.7576, "matched_fragments": 462, "total_fragments": 2066, "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": 78.6257, "matched_fragments": 449, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter africanus", "strain": "strain=DSM 12126", "accession": "GCA_900176535.1", "taxid": 151894, "species_taxid": 151894, "relation_to_type": "type", "validated": true, "ani": 78.5348, "matched_fragments": 385, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter hartonius", "strain": "strain=DSM 19033", "accession": "GCA_900107535.1", "taxid": 425514, "species_taxid": 425514, "relation_to_type": "type", "validated": true, "ani": 78.463, "matched_fragments": 207, "total_fragments": 2066, "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": 77.7078, "matched_fragments": 186, "total_fragments": 2066, "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": 77.3969, "matched_fragments": 192, "total_fragments": 2066, "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": 76.9024, "matched_fragments": 93, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter agri", "strain": "strain=R11", "accession": "GCA_009928685.1", "taxid": 2695265, "species_taxid": 2695265, "relation_to_type": "type", "validated": true, "ani": 76.3958, "matched_fragments": 70, "total_fragments": 2066, "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": 76.3494, "matched_fragments": 63, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013204795.1", "gtdb_species": "s__Pedobacter panaciterrae", "ani": 100.0, "matched_fragments": 2065, "total_fragments": 2066, "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_000523515.1", 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sp003054115", "ani": 84.7469, "matched_fragments": 1182, "total_fragments": 2066, "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_018492665.1", "gtdb_species": "s__Pedobacter sp018492665", "ani": 84.4228, "matched_fragments": 1183, "total_fragments": 2066, "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_013266735.1", "gtdb_species": "s__Pedobacter foliorum", "ani": 84.2665, "matched_fragments": 1294, "total_fragments": 2066, "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": -0.125, "cell_length": 0.301, "doubling_h": null, "growth_tmp": 24.703, "optimum_tmp": 25.0, "optimum_ph": 6.75, "genome_size": 6199746.0, "gc_content": 42.651, "coding_genes": 4725.333, "rRNA16S_genes": 4.333, "tRNA_genes": 57.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.5, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.5, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "panaciterrae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }