{ "type": "genome", "identifier": "GCF_000422945.1", "organism": "Daejeonella oryzae DSM 19973", "title": "Daejeonella oryzae DSM 19973", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000422945.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440833", "wgs_master": "AUHA00000000.1", "refseq_category": "reference genome", "taxid": "468059", "species_taxid": "1122943", "organism_name": "Daejeonella oryzae DSM 19973", "infraspecific_name": "strain=DSM 19973", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/11", "asm_name": "ASM42294v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000422945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/945/GCF_000422945.1_ASM42294v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3445768", "genome_size_ungapped": "3444648", "gc_percent": "38.000000", "replicon_count": "0", "scaffold_count": "10", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000422945.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3074", "protein_coding_gene_count": "3025", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-11", "dateModified": "2013-07-11", "datePublished": "2013-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Daejeonella oryzae DSM 19973" ], "sample_taxid": [ "468059" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.971 MB", "sample_ph_range": { "min": 68.0, "max": 68.0 }, "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)": "3445768", "Number of Sequences": "10", "Longest Sequences (bp)": "1587645", "N50 (bp)": "740939", "Gap Ratio (%)": "0.032504", "GCcontent (%)": "37.8", "Number of CDSs": "2999", "Average Protein Length": "342.0", "Coding Ratio (%)": "89.3", "Number of rRNAs": "6", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Daejeonella oryzae", "strain": "strain=DSM 19973", "accession": "GCA_000422945.1", "taxid": 1122943, "species_taxid": 1122943, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1141, 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{ "organism_name": "Mucilaginibacter boryungensis", "strain": "strain=KCTC 23157", "accession": "GCA_015221995.1", "taxid": 768480, "species_taxid": 768480, "relation_to_type": "type", "validated": true, "ani": 76.904, "matched_fragments": 60, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrotolerans", "strain": "strain=CGMCC 1.15644", "accession": "GCA_014643495.1", "taxid": 1843235, "species_taxid": 1843235, "relation_to_type": "type", "validated": true, "ani": 76.8436, "matched_fragments": 87, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter chitinilyticus", "strain": "strain=CM134L-2", "accession": "GCA_003313385.1", "taxid": 2233776, "species_taxid": 2233776, "relation_to_type": "type", "validated": true, "ani": 76.8408, "matched_fragments": 52, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter 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"accession": "GCA_003313325.1", "taxid": 600626, "species_taxid": 600626, "relation_to_type": "type", "validated": true, "ani": 76.7518, "matched_fragments": 75, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrotolerans", "strain": "strain=DSM 103236", "accession": "GCA_004340665.1", "taxid": 1843235, "species_taxid": 1843235, "relation_to_type": "type", "validated": true, "ani": 76.7409, "matched_fragments": 85, "total_fragments": 1142, "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": 76.7265, "matched_fragments": 68, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter cryotolerans", "strain": "strain=AR-2-6", "accession": "GCA_005116475.1", "taxid": 2571270, "species_taxid": 2571270, "relation_to_type": "type", "validated": true, "ani": 76.6709, "matched_fragments": 82, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter rhizosphaerae", "strain": "strain=DSM 18610", "accession": "GCA_900111155.1", "taxid": 390241, "species_taxid": 390241, "relation_to_type": "type", "validated": true, "ani": 76.6588, "matched_fragments": 75, "total_fragments": 1142, "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": 76.6576, "matched_fragments": 81, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter polytrichastri", "strain": "strain=RG4-7", "accession": "GCA_001911425.1", "taxid": 1302689, "species_taxid": 1302689, "relation_to_type": "type", "validated": true, "ani": 76.6425, "matched_fragments": 67, "total_fragments": 1142, "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": 76.4871, "matched_fragments": 70, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter polytrichastri", "strain": "strain=DSM 26907", "accession": "GCA_900116355.1", "taxid": 1302689, "species_taxid": 1302689, "relation_to_type": "type", "validated": true, "ani": 76.3598, "matched_fragments": 65, "total_fragments": 1142, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter cryophilus", "strain": "strain=AR-3-17", "accession": "GCA_005116455.1", "taxid": 2571271, "species_taxid": 2571271, "relation_to_type": "type", "validated": true, "ani": 76.1099, 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76.6566, "matched_fragments": 74, "total_fragments": 1142, "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_002151545.1", "gtdb_species": "s__Pedobacter sp002151545", "ani": 76.6275, "matched_fragments": 92, "total_fragments": 1142, "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_013408825.1", "gtdb_species": "s__Mucilaginibacter sp013408825", "ani": 76.5718, "matched_fragments": 63, 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