{ "type": "genome", "identifier": "GCF_014642175.1", "organism": "Pedobacter quisquiliarum", "title": "Pedobacter quisquiliarum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014642175.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245046", "wgs_master": "BMIL00000000.1", "refseq_category": "reference genome", "taxid": "1834438", "species_taxid": "1834438", "organism_name": "Pedobacter quisquiliarum", "infraspecific_name": "strain=CGMCC 1.15343", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1464217v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014642175.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/642/175/GCF_014642175.1_ASM1464217v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3773827", "genome_size_ungapped": "3773827", "gc_percent": "44.500000", "replicon_count": "0", "scaffold_count": "29", "contig_count": "29", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014642175.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "3385", "protein_coding_gene_count": "3322", "non_coding_gene_count": "50", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter quisquiliarum" ], "sample_taxid": [ "1834438" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.078 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)": "3773827", "Number of Sequences": "29", "Longest Sequences (bp)": "533697", "N50 (bp)": "329575", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.7", "Number of CDSs": "3291", "Average Protein Length": "344.5", "Coding Ratio (%)": "90.1", "Number of rRNAs": "0", "Number of tRNAs": "42", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter quisquiliarum", "strain": "strain=CGMCC 1.15343", "accession": "GCA_014642175.1", "taxid": 1834438, "species_taxid": 1834438, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1241, "total_fragments": 1242, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter duraquae", "strain": "strain=DSM 19034", "accession": "GCA_004362245.1", "taxid": 425511, "species_taxid": 425511, "relation_to_type": "type", "validated": true, "ani": 78.9622, "matched_fragments": 203, "total_fragments": 1242, "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": 78.8234, "matched_fragments": 139, "total_fragments": 1242, "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": 78.8184, "matched_fragments": 153, "total_fragments": 1242, "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": 78.5662, "matched_fragments": 184, "total_fragments": 1242, "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": 78.3728, "matched_fragments": 159, "total_fragments": 1242, "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": 78.3432, "matched_fragments": 162, "total_fragments": 1242, "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": 78.3107, "matched_fragments": 159, "total_fragments": 1242, "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": 78.2108, "matched_fragments": 155, "total_fragments": 1242, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter cryoconitis", "strain": "strain=DSM 14825", "accession": "GCA_003259615.1", "taxid": 188932, "species_taxid": 188932, "relation_to_type": "suspected-type", "validated": true, "ani": 78.1762, "matched_fragments": 169, "total_fragments": 1242, "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": 78.1618, "matched_fragments": 180, "total_fragments": 1242, "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": 78.1144, "matched_fragments": 190, "total_fragments": 1242, "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": 78.1143, "matched_fragments": 160, "total_fragments": 1242, "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": 77.9669, "matched_fragments": 172, "total_fragments": 1242, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter helvus", "strain": "strain=P-25", "accession": "GCA_005925325.1", "taxid": 2563444, "species_taxid": 2563444, "relation_to_type": "type", "validated": true, "ani": 77.6878, "matched_fragments": 87, "total_fragments": 1242, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.6341, "matched_fragments": 115, "total_fragments": 1242, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychroterrae", "strain": "strain=RP-1-14", "accession": "GCA_004331695.1", "taxid": 2530453, "species_taxid": 2530453, "relation_to_type": "type", "validated": true, "ani": 77.6245, "matched_fragments": 143, "total_fragments": 1242, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter soli", "strain": "strain=DSM 18609", "accession": "GCA_900101435.1", "taxid": 390242, "species_taxid": 390242, "relation_to_type": "type", "validated": true, "ani": 77.394, "matched_fragments": 123, "total_fragments": 1242, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ureilyticus", "strain": "strain=THG-T11", "accession": "GCA_005925345.1", "taxid": 1393051, "species_taxid": 1393051, "relation_to_type": "type", "validated": true, "ani": 77.2745, "matched_fragments": 93, "total_fragments": 1242, "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": 76.379, "matched_fragments": 60, "total_fragments": 1242, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014642175.1", "gtdb_species": "s__Pedobacter quisquiliarum", "ani": 100.0, "matched_fragments": 1241, "total_fragments": 1242, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.56", "min_intra_species_ani": "96.56", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCA_002320935.1", "gtdb_species": "s__Pedobacter sp002320935", "ani": 82.0073, "matched_fragments": 668, "total_fragments": 1242, "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_002333205.1", "gtdb_species": "s__Pedobacter sp002333205", "ani": 81.9019, "matched_fragments": 642, "total_fragments": 1242, "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": 78.9622, "matched_fragments": 203, "total_fragments": 1242, "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_900112985.1", "gtdb_species": "s__Pedobacter antarcticus", "ani": 78.8175, "matched_fragments": 152, "total_fragments": 1242, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "98.80", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900176505.1", "gtdb_species": "s__Pedobacter nyackensis", "ani": 78.3432, "matched_fragments": 162, "total_fragments": 1242, "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_001412655.1", "gtdb_species": "s__Pedobacter sp001412655", "ani": 78.2034, "matched_fragments": 186, "total_fragments": 1242, "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_014207135.1", "gtdb_species": "s__Pedobacter cryoconitis_D", "ani": 78.1828, "matched_fragments": 154, "total_fragments": 1242, "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_014172405.1", "gtdb_species": "s__Pedobacter gandavensis", "ani": 78.1404, "matched_fragments": 181, "total_fragments": 1242, "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": 78.1325, "matched_fragments": 189, "total_fragments": 1242, "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_001721645.1", "gtdb_species": "s__Pedobacter steynii_A", "ani": 78.0971, "matched_fragments": 190, "total_fragments": 1242, "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_001636695.1", "gtdb_species": "s__Pedobacter panaciterrae_A", "ani": 78.0936, "matched_fragments": 158, "total_fragments": 1242, "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_004364225.1", "gtdb_species": "s__Pedobacter sp004364225", "ani": 78.0761, "matched_fragments": 181, "total_fragments": 1242, "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_009765875.1", "gtdb_species": "s__Pedobacter sp009765875", "ani": 78.0244, "matched_fragments": 167, "total_fragments": 1242, "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": 78.0103, "matched_fragments": 174, "total_fragments": 1242, "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_000523515.1", "gtdb_species": "s__Pedobacter sp000523515", "ani": 77.8474, "matched_fragments": 169, "total_fragments": 1242, "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": 77.8309, "matched_fragments": 176, "total_fragments": 1242, "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": 77.805, "matched_fragments": 147, "total_fragments": 1242, "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", "quisquiliarum" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }