{ "type": "genome", "identifier": "GCF_003664035.1", "organism": "Pedobacter alluvionis", "title": "Pedobacter alluvionis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003664035.1", "bioproject": "PRJNA224116", "biosample": "SAMN05421794", "wgs_master": "RCCK00000000.1", "refseq_category": "reference genome", "taxid": "475253", "species_taxid": "475253", "organism_name": "Pedobacter alluvionis", "infraspecific_name": "strain=DSM 19624", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/15", "asm_name": "ASM366403v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003664035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/664/035/GCF_003664035.1_ASM366403v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6037645", "genome_size_ungapped": "6036062", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003664035.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "5009", "protein_coding_gene_count": "4943", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-15", "dateModified": "2018-10-15", "datePublished": "2018-10-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter alluvionis" ], "sample_taxid": [ "475253" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: northwestern Montana, Middle Fork Flathead River, Nyack Floodplain" ], "sample_host_location_id": [], "data_size": "1.702 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)": "6037645", "Number of Sequences": "18", "Longest Sequences (bp)": "1788694", "N50 (bp)": "1392503", "Gap Ratio (%)": "0.026219", "GCcontent (%)": "38.4", "Number of CDSs": "4895", "Average Protein Length": "343.7", "Coding Ratio (%)": "83.6", "Number of rRNAs": "4", "Number of tRNAs": "47", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_003664035.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2003, "total_fragments": 2003, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_004402005.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 99.9927, "matched_fragments": 2001, "total_fragments": 2003, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter borealis", "strain": "strain=DSM 19626", "accession": "GCA_000708285.2", "taxid": 475254, "species_taxid": 475254, "relation_to_type": "type", "validated": true, "ani": 86.5442, "matched_fragments": 1116, "total_fragments": 2003, "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": 86.4602, "matched_fragments": 1301, "total_fragments": 2003, "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": 86.4044, "matched_fragments": 1296, "total_fragments": 2003, "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": 85.961, "matched_fragments": 1264, "total_fragments": 2003, "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": 85.9142, "matched_fragments": 1316, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter suwonensis", "strain": "strain=DSM 18130", "accession": "GCA_900111825.1", "taxid": 332999, "species_taxid": 332999, "relation_to_type": "type", "validated": true, "ani": 83.86, "matched_fragments": 1213, "total_fragments": 2003, "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": 83.116, "matched_fragments": 1152, "total_fragments": 2003, "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": 81.6003, "matched_fragments": 989, "total_fragments": 2003, "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": 76.9112, "matched_fragments": 82, "total_fragments": 2003, "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": 76.4594, "matched_fragments": 94, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium faecale", "strain": "strain=C459-1", "accession": "GCA_016746095.1", "taxid": 2803775, "species_taxid": 2803775, "relation_to_type": "type", "validated": true, "ani": 76.3312, "matched_fragments": 55, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter gilvus", "strain": "strain=F01003", "accession": "GCA_004054195.1", "taxid": 2305909, "species_taxid": 2305909, "relation_to_type": "type", "validated": true, "ani": 76.2152, "matched_fragments": 91, "total_fragments": 2003, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003664035.1", "gtdb_species": "s__Pedobacter alluvionis", "ani": 100.0, "matched_fragments": 2003, "total_fragments": 2003, "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": "conclusive" }, { "accession": "GCF_004342125.1", "gtdb_species": "s__Pedobacter sp004342125", "ani": 94.3703, "matched_fragments": 1591, "total_fragments": 2003, "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": "GCF_014692875.1", "gtdb_species": "s__Pedobacter sp011759615", "ani": 86.3864, "matched_fragments": 1292, "total_fragments": 2003, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.16", "min_intra_species_ani": "98.15", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004310665.1", "gtdb_species": "s__Pedobacter kyonggii", "ani": 86.3853, "matched_fragments": 1298, "total_fragments": 2003, "gtdb_taxonomy": 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0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "alluvionis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }