{ "type": "genome", "identifier": "GCF_006538965.1", "organism": "Pimelobacter simplex", "title": "Pimelobacter simplex", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute of Technology and Evaluation", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006538965.1", "bioproject": "PRJNA224116", "biosample": "SAMD00097155", "wgs_master": "BJMC00000000.1", "refseq_category": "na", "taxid": "2045", "species_taxid": "2045", "organism_name": "Pimelobacter simplex", "infraspecific_name": "strain=NBRC 12069", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/06/12", "asm_name": "ASM653896v1", "asm_submitter": "National Institute of Technology and Evaluation", "gbrs_paired_asm": "GCA_006538965.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/538/965/GCF_006538965.1_ASM653896v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5615139", "genome_size_ungapped": "5615139", "gc_percent": "73.000000", "replicon_count": "0", "scaffold_count": "35", "contig_count": "35", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006538965.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "5611", "protein_coding_gene_count": "5530", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-06-12", "dateModified": "2019-06-12", "datePublished": "2019-06-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pimelobacter simplex" ], "sample_taxid": [ "2045" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.470 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)": "5615139", "Number of Sequences": "35", "Longest Sequences (bp)": "849131", "N50 (bp)": "252771", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "72.9", "Number of CDSs": "5561", "Average Protein Length": "316.3", "Coding Ratio (%)": "94.0", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pimelobacter simplex", "strain": "strain=NBRC 12069", "accession": "GCA_006538965.1", "taxid": 2045, "species_taxid": 2045, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1850, "total_fragments": 1854, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pimelobacter simplex", "strain": "strain=ATCC 6946", "accession": "GCA_900114845.1", "taxid": 2045, "species_taxid": 2045, "relation_to_type": "type", "validated": true, "ani": 99.9865, "matched_fragments": 1853, "total_fragments": 1854, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nocardioides nitrophenolicus", "strain": "strain=DSM 15529", "accession": "GCA_016907515.1", "taxid": 60489, "species_taxid": 60489, "relation_to_type": "type", "validated": true, "ani": 85.9625, "matched_fragments": 1323, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides carbamazepini", "strain": "strain=CBZ_1", "accession": "GCA_024614185.1", "taxid": 2854259, "species_taxid": 2854259, "relation_to_type": "type", "validated": true, "ani": 85.7243, "matched_fragments": 1264, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides daeguensis", "strain": "strain=2C1-5", "accession": "GCA_019192965.1", "taxid": 908359, "species_taxid": 908359, "relation_to_type": "type", "validated": true, "ani": 85.6691, "matched_fragments": 1122, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides humi", "strain": "strain=DCY24", "accession": "GCA_006494775.1", "taxid": 449461, "species_taxid": 449461, "relation_to_type": "type", "validated": true, "ani": 85.6306, "matched_fragments": 1244, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides kongjuensis", "strain": "strain=DSM 19082", "accession": "GCA_013409625.1", "taxid": 349522, "species_taxid": 349522, "relation_to_type": "type", "validated": true, "ani": 85.5799, "matched_fragments": 1255, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides aromaticivorans", "strain": "strain=DSM 15131", "accession": "GCA_013408525.1", "taxid": 200618, "species_taxid": 200618, "relation_to_type": "type", "validated": true, "ani": 84.9555, "matched_fragments": 1163, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides albidus", "strain": "strain=CCTCC AB 2015297", "accession": "GCA_006335005.1", "taxid": 1517589, "species_taxid": 1517589, "relation_to_type": "type", "validated": true, "ani": 84.9074, "matched_fragments": 1045, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides humilatus", "strain": "strain=BN130099", "accession": "GCA_008373755.1", "taxid": 2607660, "species_taxid": 2607660, "relation_to_type": "type", "validated": true, "ani": 81.4226, "matched_fragments": 858, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides sambongensis", "strain": "strain=KUDC 5002", "accession": "GCA_006494815.1", "taxid": 2589074, "species_taxid": 2589074, "relation_to_type": "type", "validated": true, "ani": 81.2169, "matched_fragments": 839, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides lacusdianchii", "strain": "strain=JXJ CY 38", "accession": "GCA_020102855.1", "taxid": 2783664, "species_taxid": 2783664, "relation_to_type": "type", "validated": true, "ani": 80.1314, "matched_fragments": 708, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nocardioides donggukensis", "strain": "strain=MJB4", "accession": "GCA_014842875.1", "taxid": 2774019, "species_taxid": 2774019, "relation_to_type": "type", "validated": true, "ani": 79.7876, "matched_fragments": 624, "total_fragments": 1854, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900114845.1", "gtdb_species": 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nitrophenolicus", "ani": 85.946, "matched_fragments": 1325, "total_fragments": 1854, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_006715725.1", "gtdb_species": "s__Nocardioides sp006715725", "ani": 85.8774, "matched_fragments": 1300, "total_fragments": 1854, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_016803235.1", "gtdb_species": "s__Nocardioides simplex_A", "ani": 85.7754, 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"gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "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_001428825.1", "gtdb_species": "s__Nocardioides sp001428825", "ani": 84.7962, "matched_fragments": 1149, "total_fragments": 1854, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.398, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 27.5, "optimum_tmp": 29.0, "optimum_ph": null, "genome_size": 5636439.167, "gc_content": 72.875, "coding_genes": 5138.333, "rRNA16S_genes": 2.0, "tRNA_genes": 47.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 1.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pimelobacter", "simplex" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }