{ "type": "genome", "identifier": "GCF_006715095.1", "organism": "Yimella lutea", "title": "Yimella lutea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_006715095.1", "bioproject": "PRJNA224116", "biosample": "SAMN11512944", "wgs_master": "VFMO00000000.1", "refseq_category": "reference genome", "taxid": "587872", "species_taxid": "587872", "organism_name": "Yimella lutea", "infraspecific_name": "strain=DSM 19828", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/07/08", "asm_name": "ASM671509v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_006715095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/006/715/095/GCF_006715095.1_ASM671509v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3533116", "genome_size_ungapped": "3533116", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_006715095.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "3461", "protein_coding_gene_count": "3308", "non_coding_gene_count": "87", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-07-08", "dateModified": "2019-07-08", "datePublished": "2019-07-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Yimella lutea" ], "sample_taxid": [ "587872" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:People's Republic of China, Yannan Province" ], "sample_host_location_id": [], "data_size": "0.963 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)": "3533116", "Number of Sequences": "1", "Longest Sequences (bp)": "3533116", "N50 (bp)": "3533116", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.9", "Number of CDSs": "3400", "Average Protein Length": "315.4", "Coding Ratio (%)": "91.1", "Number of rRNAs": "6", "Number of tRNAs": "79", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Luteipulveratus halotolerans", "strain": "strain=C296001", "accession": "GCA_001247745.1", "taxid": 1631356, "species_taxid": 1631356, "relation_to_type": "type", "validated": true, "ani": 79.5174, "matched_fragments": 476, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Barrientosiimonas humi", "strain": "strain=type strain: 39", "accession": "GCA_910573815.1", "taxid": 999931, "species_taxid": 999931, "relation_to_type": "type", "validated": true, "ani": 79.3646, "matched_fragments": 459, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Barrientosiimonas humi", "strain": "strain=DSM 24617", "accession": "GCA_006716095.1", "taxid": 999931, "species_taxid": 999931, "relation_to_type": "type", "validated": true, "ani": 79.3101, "matched_fragments": 474, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flexivirga aerilata", "strain": "strain=ID2601S", "accession": "GCA_013002715.1", "taxid": 1656889, "species_taxid": 1656889, "relation_to_type": "type", "validated": true, "ani": 79.2399, "matched_fragments": 485, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arsenicicoccus piscis", "strain": "strain=DSM 22760", "accession": "GCA_022568835.1", "taxid": 673954, "species_taxid": 673954, "relation_to_type": "type", "validated": true, "ani": 78.8666, "matched_fragments": 307, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Luteipulveratus mongoliensis", "strain": "strain=MN07-A0370", "accession": "GCA_001190945.1", "taxid": 571913, "species_taxid": 571913, "relation_to_type": "type", "validated": true, "ani": 78.866, "matched_fragments": 415, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flexivirga oryzae", "strain": "strain=DSM 105369", "accession": "GCA_014190805.1", "taxid": 1794944, "species_taxid": 1794944, "relation_to_type": "type", "validated": true, "ani": 78.8592, "matched_fragments": 426, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flexivirga endophytica", "strain": "strain=CGMCC 1.15085", "accession": "GCA_014640635.1", "taxid": 1849103, "species_taxid": 1849103, "relation_to_type": "type", "validated": true, "ani": 78.6962, "matched_fragments": 398, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dermacoccus nishinomiyaensis", "strain": "strain=FDAARGOS_1119", "accession": "GCA_016766835.1", "taxid": 1274, "species_taxid": 1274, "relation_to_type": "type", "validated": true, "ani": 78.6945, "matched_fragments": 315, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flexivirga endophytica", "strain": "strain=KCTC 39536", "accession": "GCA_014652735.1", "taxid": 1849103, "species_taxid": 1849103, "relation_to_type": "type", "validated": true, "ani": 78.6531, "matched_fragments": 406, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus duodecadis", "strain": "strain=DSM 12806", "accession": "GCA_002846495.1", "taxid": 173053, "species_taxid": 173053, "relation_to_type": "type", "validated": true, "ani": 78.6228, "matched_fragments": 321, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phycicoccus jejuensis", "strain": "strain=NRRL B-24460", "accession": "GCA_000720925.1", "taxid": 367299, "species_taxid": 367299, "relation_to_type": "type", "validated": true, "ani": 78.5252, "matched_fragments": 347, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Janibacter melonis", "strain": "strain=NBRC107855", "accession": "GCA_020567375.1", "taxid": 262209, "species_taxid": 262209, "relation_to_type": "type", "validated": true, "ani": 78.3807, "matched_fragments": 317, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Knoellia aerolata", "strain": "strain=DSM 18566", "accession": "GCA_000768695.1", "taxid": 442954, "species_taxid": 442954, "relation_to_type": "type", "validated": true, "ani": 78.3572, "matched_fragments": 300, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arsenicicoccus cauae", "strain": "strain=MKL-02", "accession": "GCA_009707125.1", "taxid": 2663847, "species_taxid": 2663847, "relation_to_type": "type", "validated": true, "ani": 78.1963, "matched_fragments": 293, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serinicoccus marinus", "strain": "strain=DSM 15273", "accession": "GCA_008386315.1", "taxid": 247333, "species_taxid": 247333, "relation_to_type": "type", "validated": true, "ani": 78.0885, "matched_fragments": 265, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium sediminis", "strain": "strain=EGI L100131", "accession": "GCA_021272345.1", "taxid": 2904603, "species_taxid": 2904603, "relation_to_type": "type", "validated": true, "ani": 77.7858, "matched_fragments": 279, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas shaoxiangyii", "strain": "strain=Z28", "accession": "GCA_004798685.1", "taxid": 2566013, "species_taxid": 2566013, "relation_to_type": "type", "validated": true, "ani": 77.078, "matched_fragments": 212, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kitasatospora griseola", "strain": "strain=JCM 3339", "accession": "GCA_014648555.1", "taxid": 2064, "species_taxid": 2064, "relation_to_type": "type", "validated": true, "ani": 76.9896, "matched_fragments": 252, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cellulomonas telluris", "strain": "strain=CPCC 204705", "accession": "GCA_004886325.1", "taxid": 2306636, "species_taxid": 2306636, "relation_to_type": "type", "validated": true, "ani": 76.7894, "matched_fragments": 213, "total_fragments": 1177, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006715095.1", "gtdb_species": "s__Yimella lutea", "ani": 100.0, "matched_fragments": 1176, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.40", "min_intra_species_ani": "98.40", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003386865.1", "gtdb_species": "s__Yimella indica", "ani": 84.4643, "matched_fragments": 804, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella", "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_017654605.1", "gtdb_species": "s__Yimella sp014530045", "ani": 81.7956, "matched_fragments": 682, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "97.58", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013135345.1", "gtdb_species": "s__Yimella sp013135345", "ani": 79.6056, "matched_fragments": 476, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Yimella", "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": "-" }, { "accession": "GCF_001247745.1", "gtdb_species": "s__Luteipulveratus halotolerans", "ani": 79.4809, "matched_fragments": 480, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus", "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_006716095.1", "gtdb_species": "s__Barrientosiimonas humi", "ani": 79.3235, "matched_fragments": 468, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013410455.1", "gtdb_species": "s__Allobranchiibius huperziae", "ani": 79.2843, "matched_fragments": 382, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.04", "min_intra_species_ani": "97.04", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013002715.1", "gtdb_species": "s__Flexivirga aerilata", "ani": 79.2594, "matched_fragments": 483, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga", "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_017565405.1", "gtdb_species": "s__Allobranchiibius sp017565405", "ani": 79.0489, "matched_fragments": 393, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Allobranchiibius", "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_006716205.1", "gtdb_species": "s__Oryzihumus leptocrescens", "ani": 78.8935, "matched_fragments": 357, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus", "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_001190945.1", "gtdb_species": "s__Luteipulveratus mongoliensis", "ani": 78.8497, "matched_fragments": 415, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus", "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_014640635.1", "gtdb_species": "s__Flexivirga endophytica", "ani": 78.6962, "matched_fragments": 398, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Flexivirga", "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": "-" }, { "accession": "GCF_002846495.1", "gtdb_species": "s__Phycicoccus duodecadis", "ani": 78.6105, "matched_fragments": 322, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus", "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_002754615.1", "gtdb_species": "s__Kitasatospora sp002754615", "ani": 77.1724, "matched_fragments": 258, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014648555.1", "gtdb_species": "s__Kitasatospora griseola", "ani": 76.97, "matched_fragments": 254, "total_fragments": 1177, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "97.68", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.125, "cell_length": 0.153, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.0, "optimum_ph": 6.5, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Yimella", "lutea" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }