{ "type": "genome", "identifier": "GCF_900176505.1", "organism": "Pedobacter nyackensis", "title": "Pedobacter nyackensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900176505.1", "bioproject": "PRJNA224116", "biosample": "SAMN04488101", "wgs_master": "FWYB00000000.1", "refseq_category": "reference genome", "taxid": "475255", "species_taxid": "475255", "organism_name": "Pedobacter nyackensis", "infraspecific_name": "strain=DSM 19625", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/04/08", "asm_name": "IMG-taxon 2622736511 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900176505.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/176/505/GCF_900176505.1_IMG-taxon_2622736511_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6077111", "genome_size_ungapped": "6076301", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "33", "contig_count": "33", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900176505.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "4991", "protein_coding_gene_count": "4902", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-04-08", "dateModified": "2017-04-08", "datePublished": "2017-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter nyackensis" ], "sample_taxid": [ "475255" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.725 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)": "6077111", "Number of Sequences": "33", "Longest Sequences (bp)": "1005999", "N50 (bp)": "295816", "Gap Ratio (%)": "0.013329", "GCcontent (%)": "39.5", "Number of CDSs": "4856", "Average Protein Length": "377.1", "Coding Ratio (%)": "90.4", "Number of rRNAs": "6", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter nyackensis", "strain": "strain=DSM 19625", "accession": "GCA_900176505.1", "taxid": 475255, "species_taxid": 475255, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2008, "total_fragments": 2009, "ani_threshold": 95, "status": "conclusive" }, { "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": 82.461, "matched_fragments": 975, "total_fragments": 2009, "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": 80.315, "matched_fragments": 788, "total_fragments": 2009, "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": 79.747, "matched_fragments": 604, "total_fragments": 2009, "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": 79.6947, "matched_fragments": 610, "total_fragments": 2009, "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": 79.3707, "matched_fragments": 507, "total_fragments": 2009, "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": 79.276, "matched_fragments": 421, "total_fragments": 2009, "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": 79.2237, "matched_fragments": 398, "total_fragments": 2009, "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": 79.1364, "matched_fragments": 487, "total_fragments": 2009, "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": 78.9704, "matched_fragments": 424, "total_fragments": 2009, "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": 78.6502, "matched_fragments": 345, "total_fragments": 2009, "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": 76.4136, "matched_fragments": 104, "total_fragments": 2009, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900176505.1", "gtdb_species": "s__Pedobacter nyackensis", "ani": 100.0, "matched_fragments": 2008, "total_fragments": 2009, "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_004331685.1", "gtdb_species": "s__Pedobacter sp004331685", "ani": 82.4652, "matched_fragments": 975, "total_fragments": 2009, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.88", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900100435.1", "gtdb_species": "s__Pedobacter sp900100435", "ani": 82.3324, "matched_fragments": 987, "total_fragments": 2009, "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_900564155.1", "gtdb_species": "s__Pedobacter sp900564155", "ani": 80.3067, "matched_fragments": 788, "total_fragments": 2009, "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_000023825.1", "gtdb_species": "s__Pedobacter heparinus", "ani": 79.6988, "matched_fragments": 611, "total_fragments": 2009, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003054115.1", "gtdb_species": "s__Pedobacter sp003054115", "ani": 79.3722, "matched_fragments": 518, "total_fragments": 2009, "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": 79.3606, "matched_fragments": 508, "total_fragments": 2009, "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": 79.3395, "matched_fragments": 487, "total_fragments": 2009, "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_005116445.1", "gtdb_species": "s__Pedobacter sp005116445", "ani": 79.2188, "matched_fragments": 399, "total_fragments": 2009, "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_014472395.1", "gtdb_species": "s__Pedobacter sp014472395", "ani": 79.1681, "matched_fragments": 392, "total_fragments": 2009, "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": 79.1105, "matched_fragments": 522, "total_fragments": 2009, "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_002736205.1", "gtdb_species": "s__Pedobacter ginsengisoli", "ani": 79.0413, "matched_fragments": 464, "total_fragments": 2009, "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": 78.9136, "matched_fragments": 397, "total_fragments": 2009, "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": -0.347, "cell_length": 0.397, "doubling_h": null, "growth_tmp": 20.0, "optimum_tmp": 17.0, "optimum_ph": 7.5, "genome_size": 6077111.0, "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": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "nyackensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }