{ "type": "genome", "identifier": "GCF_008831125.1", "organism": "Pseudoclavibacter caeni", "title": "Pseudoclavibacter caeni", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Research Institute of Forest Ecology Environment and Protection", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008831125.1", "bioproject": "PRJNA224116", "biosample": "SAMN12810919", "wgs_master": "WBKA00000000.1", "refseq_category": "reference genome", "taxid": "908846", "species_taxid": "908846", "organism_name": "Pseudoclavibacter caeni", "infraspecific_name": "strain=JCM 16921", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/10/06", "asm_name": "ASM883112v1", "asm_submitter": "Research Institute of Forest Ecology Environment and Protection", "gbrs_paired_asm": "GCA_008831125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/831/125/GCF_008831125.1_ASM883112v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2059739", "genome_size_ungapped": "2059729", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "11", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008831125.1-RS_2024_11_18", "annotation_date": "2024-11-18", "total_gene_count": "1806", "protein_coding_gene_count": "1725", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-10-06", "dateModified": "2019-10-06", "datePublished": "2019-10-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoclavibacter caeni" ], "sample_taxid": [ "908846" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.549 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)": "2059739", "Number of Sequences": "11", "Longest Sequences (bp)": "569632", "N50 (bp)": "365083", "Gap Ratio (%)": "0.000485", "GCcontent (%)": "71.2", "Number of CDSs": "1770", "Average Protein Length": "345.9", "Coding Ratio (%)": "89.2", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoclavibacter caeni", "strain": "strain=JCM 16921", "accession": "GCA_008831125.1", "taxid": 908846, "species_taxid": 908846, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 679, "total_fragments": 680, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoclavibacter caeni", "strain": "strain=DSM 26484", "accession": "GCA_013410595.1", "taxid": 908846, "species_taxid": 908846, "relation_to_type": "type", "validated": true, "ani": 99.9988, "matched_fragments": 679, "total_fragments": 680, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoclavibacter soli", "strain": "strain=DSM 23366", "accession": "GCA_000423505.1", "taxid": 452623, "species_taxid": 452623, "relation_to_type": "type", "validated": true, "ani": 78.9062, "matched_fragments": 266, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces badenianii", "strain": "strain=MF30-A", "accession": "GCA_003070885.1", "taxid": 2080742, "species_taxid": 2080742, "relation_to_type": "type", "validated": true, "ani": 77.5071, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces luteolus", "strain": "strain=JCM 11431", "accession": "GCA_009729855.1", "taxid": 88373, "species_taxid": 88373, "relation_to_type": "type", "validated": true, "ani": 77.3866, "matched_fragments": 251, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curtobacterium flaccumfaciens", "strain": "strain=LMG3645", "accession": "GCA_024997845.1", "taxid": 2035, "species_taxid": 2035, "relation_to_type": "suspected-type", "validated": true, "ani": 77.3794, "matched_fragments": 207, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rathayibacter caricis", "strain": "strain=DSM 15933", "accession": "GCA_003044275.1", "taxid": 110936, "species_taxid": 110936, "relation_to_type": "type", "validated": true, "ani": 77.3571, "matched_fragments": 223, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces italicus", "strain": "strain=JCM 14320", "accession": "GCA_009749375.1", "taxid": 279572, "species_taxid": 279572, "relation_to_type": "type", "validated": true, "ani": 77.3419, "matched_fragments": 230, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cnuibacter physcomitrellae", "strain": "strain=CGMCC 1.15041", "accession": "GCA_014640535.1", "taxid": 1619308, "species_taxid": 1619308, "relation_to_type": "type", "validated": true, "ani": 77.3387, "matched_fragments": 218, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium paulum", "strain": "strain=2C", "accession": "GCA_015707995.1", "taxid": 2707006, "species_taxid": 2707006, "relation_to_type": "type", "validated": true, "ani": 77.337, "matched_fragments": 206, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Curtobacterium citreum", "strain": "strain=LMG8786T", "accession": "GCA_024997915.1", "taxid": 2036, "species_taxid": 2036, "relation_to_type": "type", "validated": true, "ani": 77.3086, "matched_fragments": 202, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces bauzanensis", "strain": "strain=CGMCC 1.8984", "accession": "GCA_014645655.1", "taxid": 1308924, "species_taxid": 1308924, "relation_to_type": "type", "validated": true, "ani": 77.3067, "matched_fragments": 206, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Leucobacter chromiisoli", "strain": "strain=CSA1", "accession": "GCA_016522505.1", "taxid": 2796471, "species_taxid": 2796471, "relation_to_type": "type", "validated": true, "ani": 77.2763, "matched_fragments": 197, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amnibacterium kyonggiense", "strain": "strain=DSM 24782", "accession": "GCA_004364555.1", "taxid": 595671, "species_taxid": 595671, "relation_to_type": "type", "validated": true, "ani": 77.1712, "matched_fragments": 223, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kocuria sediminis", "strain": "strain=JCM 17929", "accession": "GCA_009735315.1", "taxid": 1038857, "species_taxid": 1038857, "relation_to_type": "type", "validated": true, "ani": 77.1278, "matched_fragments": 175, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clavibacter phaseoli", "strain": "strain=LPPA 982", "accession": "GCA_021922925.1", "taxid": 1734031, "species_taxid": 1734031, "relation_to_type": "type", "validated": true, "ani": 76.956, "matched_fragments": 229, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas palmilytica", "strain": "strain=EW123", "accession": "GCA_021590045.1", "taxid": 2608402, "species_taxid": 2608402, "relation_to_type": "type", "validated": true, "ani": 76.7997, "matched_fragments": 215, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Actinotalea solisilvae", "strain": "strain=KACC 19191", "accession": "GCA_016464425.1", "taxid": 2072922, "species_taxid": 2072922, "relation_to_type": "type", "validated": true, "ani": 76.4888, "matched_fragments": 206, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Occultella glacieicola", "strain": "strain=T3246-1", "accession": "GCA_004353825.1", "taxid": 2518684, "species_taxid": 2518684, "relation_to_type": "type", "validated": true, "ani": 76.4269, "matched_fragments": 144, "total_fragments": 680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Corynebacterium sanguinis", "strain": "strain=CCUG 58655", "accession": "GCA_007641235.1", "taxid": 2594913, "species_taxid": 2594913, "relation_to_type": "type", "validated": true, "ani": 76.1446, 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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": [ "Pseudoclavibacter", "caeni" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }