{ "type": "genome", "identifier": "GCF_004331645.1", "organism": "Pedobacter frigiditerrae", "title": "Pedobacter frigiditerrae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kyonggi University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004331645.1", "bioproject": "PRJNA224116", "biosample": "SAMN11032488", "wgs_master": "SJSK00000000.1", "refseq_category": "reference genome", "taxid": "2530452", "species_taxid": "2530452", "organism_name": "Pedobacter frigiditerrae", "infraspecific_name": "strain=RP-1-13", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/06", "asm_name": "ASM433164v1", "asm_submitter": "Kyonggi University", "gbrs_paired_asm": "GCA_004331645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/331/645/GCF_004331645.1_ASM433164v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5810223", "genome_size_ungapped": "5810223", "gc_percent": "36.000000", "replicon_count": "0", "scaffold_count": "13", "contig_count": "13", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004331645.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4804", "protein_coding_gene_count": "4733", "non_coding_gene_count": "49", "pubmed_id": "32160145" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-06", "dateModified": "2019-03-06", "datePublished": "2019-03-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter frigiditerrae" ], "sample_taxid": [ "2530452" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Norway: Svalbard" ], "sample_host_location_id": [], "data_size": "1.631 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)": "5810223", "Number of Sequences": "13", "Longest Sequences (bp)": "1676138", "N50 (bp)": "819745", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.9", "Number of CDSs": "4726", "Average Protein Length": "360.3", "Coding Ratio (%)": "87.9", "Number of rRNAs": "6", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter frigiditerrae", "strain": "strain=RP-1-13", "accession": "GCA_004331645.1", "taxid": 2530452, "species_taxid": 2530452, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1929, "total_fragments": 1929, "ani_threshold": 95, "status": "conclusive" }, { "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": 81.6161, "matched_fragments": 913, "total_fragments": 1929, "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": 81.0618, "matched_fragments": 747, "total_fragments": 1929, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter cryotolerans", "strain": "strain=AR-2-6", "accession": "GCA_005116475.1", "taxid": 2571270, "species_taxid": 2571270, "relation_to_type": "type", "validated": true, "ani": 80.2978, "matched_fragments": 729, "total_fragments": 1929, "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": 79.0885, "matched_fragments": 533, "total_fragments": 1929, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter insulae", "strain": "strain=DSM 18684", "accession": "GCA_900113525.1", "taxid": 414048, "species_taxid": 414048, "relation_to_type": "type", "validated": true, "ani": 78.5285, "matched_fragments": 448, "total_fragments": 1929, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter xixiisoli", "strain": "strain=CGMCC 1.12803", "accession": "GCA_900215335.1", "taxid": 1476464, "species_taxid": 1476464, "relation_to_type": "type", "validated": true, "ani": 77.9993, "matched_fragments": 352, "total_fragments": 1929, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter xixiisoli", "strain": "strain=S27", "accession": "GCA_005925365.1", "taxid": 1476464, "species_taxid": 1476464, "relation_to_type": "type", "validated": true, "ani": 77.9632, "matched_fragments": 358, "total_fragments": 1929, "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": 77.8979, "matched_fragments": 187, "total_fragments": 1929, "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": 77.8793, "matched_fragments": 360, "total_fragments": 1929, "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": 77.4233, "matched_fragments": 274, "total_fragments": 1929, "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": 76.8748, "matched_fragments": 67, "total_fragments": 1929, "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": 76.4673, "matched_fragments": 148, "total_fragments": 1929, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter segetis", "strain": "strain=SD-b", "accession": "GCA_016623585.1", "taxid": 2793069, "species_taxid": 2793069, "relation_to_type": "type", "validated": true, "ani": 76.0795, "matched_fragments": 92, "total_fragments": 1929, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004331645.1", "gtdb_species": "s__Pedobacter sp004331645", "ani": 100.0, "matched_fragments": 1929, "total_fragments": 1929, "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": "GCA_004295885.1", "gtdb_species": "s__Pedobacter sp004295885", "ani": 85.3359, "matched_fragments": 772, "total_fragments": 1929, "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_005116505.1", "gtdb_species": "s__Pedobacter sp005116505", "ani": 81.6209, "matched_fragments": 913, "total_fragments": 1929, "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_014172375.1", "gtdb_species": "s__Pedobacter planticolens", "ani": 81.0733, "matched_fragments": 747, "total_fragments": 1929, "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_013204825.1", "gtdb_species": "s__Pedobacter boryungensis", "ani": 80.6488, "matched_fragments": 694, "total_fragments": 1929, "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_005116475.1", "gtdb_species": "s__Pedobacter sp005116475", "ani": 80.2896, "matched_fragments": 730, "total_fragments": 1929, "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_001412215.1", "gtdb_species": "s__Pedobacter sp001412215", "ani": 79.7024, "matched_fragments": 622, "total_fragments": 1929, "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_003054115.1", "gtdb_species": "s__Pedobacter sp003054115", "ani": 78.1937, "matched_fragments": 237, "total_fragments": 1929, "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_014635725.1", "gtdb_species": "s__Pedobacter mendelii", "ani": 77.5522, "matched_fragments": 298, "total_fragments": 1929, "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", "frigiditerrae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }