{ "type": "genome", "identifier": "GCF_009674725.1", "organism": "Pedobacter petrophilus", "title": "Pedobacter petrophilus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Lycoming College", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009674725.1", "bioproject": "PRJNA224116", "biosample": "SAMN13262548", "wgs_master": "WKKH00000000.1", "refseq_category": "na", "taxid": "1908241", "species_taxid": "1908241", "organism_name": "Pedobacter petrophilus", "infraspecific_name": "strain=LMG 29686", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/11/19", "asm_name": "ASM967472v1", "asm_submitter": "Lycoming College", "gbrs_paired_asm": "GCA_009674725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/674/725/GCF_009674725.1_ASM967472v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5474439", "genome_size_ungapped": "5474439", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "148", "contig_count": "148", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009674725.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "4740", "protein_coding_gene_count": "4656", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-11-19", "dateModified": "2019-11-19", "datePublished": "2019-11-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter petrophilus" ], "sample_taxid": [ "1908241" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica: Devils Rocks, James Ross Island" ], "sample_host_location_id": [], "data_size": "1.549 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)": "5474439", "Number of Sequences": "148", "Longest Sequences (bp)": "306288", "N50 (bp)": "111074", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.6", "Number of CDSs": "4564", "Average Protein Length": "338.1", "Coding Ratio (%)": "84.6", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter petrophilus", "strain": "strain=LMG 29686", "accession": "GCA_009674725.1", "taxid": 1908241, "species_taxid": 1908241, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1760, "total_fragments": 1765, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter psychrotolerans", "strain": "strain=DSM 103236", "accession": "GCA_004340665.1", "taxid": 1843235, "species_taxid": 1843235, "relation_to_type": "type", "validated": true, "ani": 81.5954, "matched_fragments": 995, "total_fragments": 1765, "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": 81.5691, "matched_fragments": 986, "total_fragments": 1765, "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": 80.2697, "matched_fragments": 641, "total_fragments": 1765, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter agri", "strain": "strain=PB92", "accession": "GCA_000258495.1", "taxid": 454586, "species_taxid": 454586, "relation_to_type": "type", "validated": true, "ani": 80.2678, "matched_fragments": 625, "total_fragments": 1765, "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": 80.2423, "matched_fragments": 681, "total_fragments": 1765, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_004402005.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 80.1825, "matched_fragments": 697, "total_fragments": 1765, "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": 80.0542, "matched_fragments": 634, "total_fragments": 1765, "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": 79.9578, "matched_fragments": 672, "total_fragments": 1765, "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": 79.9487, "matched_fragments": 722, "total_fragments": 1765, "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": 79.7812, "matched_fragments": 641, "total_fragments": 1765, "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": 79.7558, "matched_fragments": 671, "total_fragments": 1765, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter yonginense", "strain": "strain=KCTC22721", "accession": "GCA_003173595.1", "taxid": 651869, "species_taxid": 651869, "relation_to_type": "type", "validated": true, "ani": 79.4486, "matched_fragments": 536, "total_fragments": 1765, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter mucosus", "strain": "strain=Q8-18", "accession": "GCA_022200785.1", "taxid": 2895286, "species_taxid": 2895286, "relation_to_type": "type", "validated": true, "ani": 79.3218, "matched_fragments": 545, "total_fragments": 1765, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter robiniae", "strain": "strain=F39-2", "accession": "GCA_012849215.1", "taxid": 2728022, "species_taxid": 2728022, "relation_to_type": "type", "validated": true, "ani": 77.052, "matched_fragments": 53, "total_fragments": 1765, "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": 76.2474, "matched_fragments": 65, "total_fragments": 1765, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009674725.1", "gtdb_species": "s__Pedobacter petrophilus", "ani": 100.0, "matched_fragments": 1760, "total_fragments": 1765, "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_004340665.1", "gtdb_species": "s__Pedobacter psychrotolerans", "ani": 81.5841, "matched_fragments": 997, "total_fragments": 1765, "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_000708265.2", "gtdb_species": "s__Pedobacter sp000708265", "ani": 81.282, "matched_fragments": 990, "total_fragments": 1765, "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_002197755.1", "gtdb_species": "s__Pedobacter sp002197755", "ani": 81.2137, "matched_fragments": 944, "total_fragments": 1765, "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": 80.2599, "matched_fragments": 627, "total_fragments": 1765, "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_003664035.1", "gtdb_species": "s__Pedobacter alluvionis", "ani": 80.2296, "matched_fragments": 684, "total_fragments": 1765, "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": "GCA_002151545.1", "gtdb_species": "s__Pedobacter sp002151545", "ani": 80.055, "matched_fragments": 673, "total_fragments": 1765, "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_003339865.1", "gtdb_species": "s__Pedobacter chinensis", "ani": 80.0487, "matched_fragments": 667, "total_fragments": 1765, "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_004342125.1", "gtdb_species": "s__Pedobacter sp004342125", "ani": 80.0259, "matched_fragments": 722, "total_fragments": 1765, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.29", "min_intra_species_ani": "95.29", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018613605.1", "gtdb_species": "s__Pedobacter sp018613605", "ani": 79.998, "matched_fragments": 674, "total_fragments": 1765, "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": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004331675.1", "gtdb_species": "s__Pedobacter sp004331675", "ani": 79.95, "matched_fragments": 673, "total_fragments": 1765, "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": 79.8989, "matched_fragments": 710, "total_fragments": 1765, "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_003725795.1", "gtdb_species": "s__Pedobacter jejuensis", "ani": 79.6579, "matched_fragments": 624, "total_fragments": 1765, "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": 79.528, "matched_fragments": 452, "total_fragments": 1765, "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", "petrophilus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }