{ "type": "genome", "identifier": "GCF_014196715.1", "organism": "Pedobacter zeae", "title": "Pedobacter zeae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014196715.1", "bioproject": "PRJNA224116", "biosample": "SAMN13172622", "wgs_master": "JACIEF000000000.1", "refseq_category": "na", "taxid": "1737356", "species_taxid": "1737356", "organism_name": "Pedobacter zeae", "infraspecific_name": "strain=DSM 100774", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/08/14", "asm_name": "ASM1419671v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_014196715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/196/715/GCF_014196715.1_ASM1419671v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5444802", "genome_size_ungapped": "5444411", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "11", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014196715.1-RS_2024_09_26", "annotation_date": "2024-09-26", "total_gene_count": "4587", "protein_coding_gene_count": "4519", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-08-14", "dateModified": "2020-08-14", "datePublished": "2020-08-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter zeae" ], "sample_taxid": [ "1737356" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.534 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)": "5444802", "Number of Sequences": "11", "Longest Sequences (bp)": "1606962", "N50 (bp)": "1517507", "Gap Ratio (%)": "0.007181", "GCcontent (%)": "40.3", "Number of CDSs": "4506", "Average Protein Length": "347.9", "Coding Ratio (%)": "86.4", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter zeae", "strain": "strain=DSM 100774", "accession": "GCA_014196715.1", "taxid": 1737356, "species_taxid": 1737356, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1808, "total_fragments": 1808, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter zeae", "strain": "strain=CGMCC 1.15287", "accession": "GCA_014641575.1", "taxid": 1737356, "species_taxid": 1737356, "relation_to_type": "type", "validated": true, "ani": 99.9989, "matched_fragments": 1806, "total_fragments": 1808, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter miscanthi", "strain": "strain=RS10", "accession": "GCA_003315595.1", "taxid": 2259170, "species_taxid": 2259170, "relation_to_type": "type", "validated": true, "ani": 83.1291, "matched_fragments": 1154, "total_fragments": 1808, "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": 83.1072, "matched_fragments": 1174, "total_fragments": 1808, "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": 83.0705, "matched_fragments": 1056, "total_fragments": 1808, "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": 82.9318, "matched_fragments": 1227, "total_fragments": 1808, "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": 82.7804, "matched_fragments": 1152, "total_fragments": 1808, "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": 82.6146, "matched_fragments": 1089, "total_fragments": 1808, "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": 82.2596, "matched_fragments": 1032, "total_fragments": 1808, "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": 82.2417, "matched_fragments": 1062, "total_fragments": 1808, "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": 82.0364, "matched_fragments": 1079, "total_fragments": 1808, "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": 81.8246, "matched_fragments": 1028, "total_fragments": 1808, "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": 79.6523, "matched_fragments": 624, "total_fragments": 1808, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter mucosus", "strain": "strain=Q8-18", "accession": "GCA_022200785.1", "taxid": 2895286, "species_taxid": 2895286, "relation_to_type": "type", "validated": true, "ani": 78.813, "matched_fragments": 460, "total_fragments": 1808, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobacterium prati", "strain": "strain=arapr2", "accession": "GCA_013167215.1", "taxid": 2737006, "species_taxid": 2737006, "relation_to_type": "type", "validated": true, "ani": 76.5863, "matched_fragments": 54, "total_fragments": 1808, "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": 76.5161, "matched_fragments": 83, "total_fragments": 1808, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014196715.1", "gtdb_species": "s__Pedobacter zeae", "ani": 100.0, "matched_fragments": 1808, "total_fragments": 1808, "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": "GCA_017745075.1", "gtdb_species": "s__Pedobacter sp017745075", "ani": 89.3298, "matched_fragments": 1510, "total_fragments": 1808, "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_014692875.1", "gtdb_species": "s__Pedobacter sp011759615", "ani": 83.8146, "matched_fragments": 1306, "total_fragments": 1808, 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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_000633455.1", "gtdb_species": "s__Pedobacter jeongneungensis", "ani": 83.6408, "matched_fragments": 1180, "total_fragments": 1808, "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_003315595.1", "gtdb_species": "s__Pedobacter miscanthi", "ani": 83.1365, "matched_fragments": 1154, "total_fragments": 1808, "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_002432345.1", "gtdb_species": "s__Pedobacter sp002432345", "ani": 83.126, "matched_fragments": 1037, "total_fragments": 1808, "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_900100705.1", "gtdb_species": "s__Pedobacter terrae", "ani": 82.6175, "matched_fragments": 1090, "total_fragments": 1808, "gtdb_taxonomy": 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