{ "type": "genome", "identifier": "GCF_004335085.1", "organism": "Pedobacter nototheniae", "title": "Pedobacter nototheniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Universidad Andres Bello", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004335085.1", "bioproject": "PRJNA224116", "biosample": "SAMN10430848", "wgs_master": "RQRS00000000.1", "refseq_category": "reference genome", "taxid": "2488994", "species_taxid": "2488994", "organism_name": "Pedobacter nototheniae", "infraspecific_name": "strain=36B243", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/08", "asm_name": "ASM433508v1", "asm_submitter": "Universidad Andres Bello", "gbrs_paired_asm": "GCA_004335085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/335/085/GCF_004335085.1_ASM433508v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5263887", "genome_size_ungapped": "5263857", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "106", "contig_count": "106", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004335085.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4580", "protein_coding_gene_count": "4511", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-08", "dateModified": "2019-03-08", "datePublished": "2019-03-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter nototheniae" ], "sample_taxid": [ "2488994" ], "sample_host_organism": [ "Notothenia coriiceps (black rock cod)" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica: Chile" ], "sample_host_location_id": [], "data_size": "1.475 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)": "5263887", "Number of Sequences": "106", "Longest Sequences (bp)": "451764", "N50 (bp)": "174373", "Gap Ratio (%)": "0.001330", "GCcontent (%)": "35.4", "Number of CDSs": "4431", "Average Protein Length": "340.9", "Coding Ratio (%)": "86.1", "Number of rRNAs": "4", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter nototheniae", "strain": "strain=36B243", "accession": "GCA_004335085.1", "taxid": 2488994, "species_taxid": 2488994, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1714, "total_fragments": 1717, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter fastidiosus", "strain": "strain=CCM 8938", "accession": "GCA_014306625.1", "taxid": 2765361, "species_taxid": 2765361, "relation_to_type": "type", "validated": true, "ani": 80.2992, "matched_fragments": 685, "total_fragments": 1717, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter chinensis", "strain": "strain=JDX94", "accession": "GCA_003339865.1", "taxid": 2282421, "species_taxid": 2282421, "relation_to_type": "type", "validated": true, "ani": 80.2864, "matched_fragments": 635, "total_fragments": 1717, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter kyonggii", "strain": "strain=K-4-11-1", "accession": "GCA_004310665.1", "taxid": 1926871, "species_taxid": 1926871, "relation_to_type": "type", "validated": true, "ani": 80.212, "matched_fragments": 642, "total_fragments": 1717, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrodurus", "strain": "strain=RP-3-21", "accession": "GCA_004331735.1", "taxid": 2530456, "species_taxid": 2530456, "relation_to_type": "type", "validated": true, "ani": 80.1291, "matched_fragments": 647, "total_fragments": 1717, "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": 80.0963, "matched_fragments": 630, "total_fragments": 1717, "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": 80.0746, "matched_fragments": 671, "total_fragments": 1717, "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": 80.0654, "matched_fragments": 627, "total_fragments": 1717, "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": 80.0261, "matched_fragments": 635, "total_fragments": 1717, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter kyungheensis", "strain": "strain=KACC 16221", "accession": "GCA_000812965.1", "taxid": 1069985, "species_taxid": 1069985, "relation_to_type": "type", "validated": true, "ani": 79.981, "matched_fragments": 637, "total_fragments": 1717, "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": 79.9487, "matched_fragments": 621, "total_fragments": 1717, "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": 79.7314, "matched_fragments": 644, "total_fragments": 1717, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter terrae", "strain": "strain=DSM 17933", "accession": "GCA_900100705.1", "taxid": 405671, "species_taxid": 405671, "relation_to_type": "type", "validated": true, "ani": 79.7146, "matched_fragments": 625, "total_fragments": 1717, "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": 79.6628, "matched_fragments": 603, "total_fragments": 1717, "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": 79.4733, "matched_fragments": 623, "total_fragments": 1717, "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": 76.9613, "matched_fragments": 84, "total_fragments": 1717, "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": 76.6625, "matched_fragments": 64, "total_fragments": 1717, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004335085.1", "gtdb_species": "s__Pedobacter nototheniae", "ani": 100.0, "matched_fragments": 1714, "total_fragments": 1717, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.28", "min_intra_species_ani": "98.28", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003387415.1", "gtdb_species": "s__Pedobacter sp003387415", "ani": 80.3472, "matched_fragments": 646, "total_fragments": 1717, "gtdb_taxonomy": 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"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_002151545.1", "gtdb_species": "s__Pedobacter sp002151545", "ani": 80.1475, "matched_fragments": 634, "total_fragments": 1717, "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_004331735.1", "gtdb_species": "s__Pedobacter sp004331735", "ani": 80.1225, "matched_fragments": 649, "total_fragments": 1717, "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_003054145.1", "gtdb_species": "s__Pedobacter sp003054145", "ani": 80.0796, "matched_fragments": 651, "total_fragments": 1717, "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_000708285.2", "gtdb_species": "s__Pedobacter borealis", "ani": 80.0795, "matched_fragments": 632, "total_fragments": 1717, "gtdb_taxonomy": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "nototheniae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }