{ "type": "genome", "identifier": "GCF_017876515.1", "organism": "Brachybacterium fresconis", "title": "Brachybacterium fresconis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017876515.1", "bioproject": "PRJNA224116", "biosample": "SAMN17673569", "wgs_master": "JAGIOC000000000.1", "refseq_category": "reference genome", "taxid": "173363", "species_taxid": "173363", "organism_name": "Brachybacterium fresconis", "infraspecific_name": "strain=DSM 14564", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/04/08", "asm_name": "ASM1787651v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_017876515.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/876/515/GCF_017876515.1_ASM1787651v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4628988", "genome_size_ungapped": "4628988", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017876515.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "4118", "protein_coding_gene_count": "4025", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-04-08", "dateModified": "2021-04-08", "datePublished": "2021-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Brachybacterium fresconis" ], "sample_taxid": [ "173363" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Austria" ], "sample_host_location_id": [], "data_size": "1.237 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)": "4628988", "Number of Sequences": "2", "Longest Sequences (bp)": "4563501", "N50 (bp)": "4563501", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "70.5", "Number of CDSs": "4133", "Average Protein Length": "334.7", "Coding Ratio (%)": "89.7", "Number of rRNAs": "9", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Brachybacterium fresconis", "strain": "strain=DSM 14564", "accession": "GCA_017876515.1", "taxid": 173363, "species_taxid": 173363, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1542, "total_fragments": 1542, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Brachybacterium sacelli", "strain": "strain=DSM 14566", "accession": "GCA_017876545.1", "taxid": 173364, "species_taxid": 173364, "relation_to_type": "type", "validated": true, "ani": 87.0345, "matched_fragments": 1142, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium faecium", "strain": "strain=DSM 4810", "accession": "GCA_000023405.1", "taxid": 43669, "species_taxid": 43669, "relation_to_type": "type", "validated": true, "ani": 83.3263, "matched_fragments": 893, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium vulturis", "strain": "strain=VM2412", "accession": "GCA_002407185.1", "taxid": 2017484, "species_taxid": 2017484, "relation_to_type": "type", "validated": true, "ani": 83.22, "matched_fragments": 880, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium massiliense", "strain": "strain=mt5", "accession": "GCA_900184245.1", "taxid": 1755098, "species_taxid": 1755098, "relation_to_type": "type", "validated": true, "ani": 83.1453, "matched_fragments": 849, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium avium", "strain": "strain=VR2415", "accession": "GCA_002216795.1", "taxid": 2017485, "species_taxid": 2017485, "relation_to_type": "type", "validated": true, "ani": 83.084, "matched_fragments": 848, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium ginsengisoli", "strain": "strain=DCY80", "accession": "GCA_002407065.1", "taxid": 1331682, "species_taxid": 1331682, "relation_to_type": "type", "validated": true, "ani": 82.9395, "matched_fragments": 922, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium aquaticum", "strain": "strain=DSM 28796", "accession": "GCA_014204755.1", "taxid": 1432564, "species_taxid": 1432564, "relation_to_type": "type", "validated": true, "ani": 82.8143, "matched_fragments": 795, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium saurashtrense", "strain": "strain=DSM 23186", "accession": "GCA_003994295.1", "taxid": 556288, "species_taxid": 556288, "relation_to_type": "type", "validated": true, "ani": 82.7322, "matched_fragments": 877, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium squillarum", "strain": "strain=M-6-3", "accession": "GCA_000225825.2", "taxid": 661979, "species_taxid": 661979, "relation_to_type": "type", "validated": true, "ani": 82.2831, "matched_fragments": 726, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium epidermidis", "strain": "strain=Marseille-Q2903", "accession": "GCA_015209585.1", "taxid": 2781983, "species_taxid": 2781983, "relation_to_type": "type", "validated": true, "ani": 81.3064, "matched_fragments": 654, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium halotolerans subsp. kimchii", "strain": "strain=CBA3105", "accession": "GCA_020792675.1", "taxid": 2887346, "species_taxid": 2795215, "relation_to_type": "type", "validated": true, "ani": 80.5694, "matched_fragments": 691, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brachybacterium kimchii", "strain": "strain=CBA3104", "accession": "GCA_023373525.1", "taxid": 2942909, "species_taxid": 2942909, "relation_to_type": "type", "validated": true, "ani": 80.5126, "matched_fragments": 707, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Occultella aeris", "strain": "strain=CIP 111667", "accession": "GCA_902703175.1", "taxid": 2761496, "species_taxid": 2761496, "relation_to_type": "type", "validated": true, "ani": 76.7294, "matched_fragments": 318, "total_fragments": 1542, "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": 76.6333, "matched_fragments": 312, "total_fragments": 1542, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017876515.1", "gtdb_species": "s__Brachybacterium fresconis", "ani": 100.0, "matched_fragments": 1541, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "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": "conclusive" }, { "accession": "GCF_001969445.1", "gtdb_species": "s__Brachybacterium sp001969445", "ani": 91.4382, "matched_fragments": 1208, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "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_017876545.1", "gtdb_species": "s__Brachybacterium sacelli", "ani": 87.0282, "matched_fragments": 1142, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "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_014897585.1", "gtdb_species": "s__Brachybacterium tyrofermentans", "ani": 83.7946, "matched_fragments": 1010, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.83", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014897705.1", "gtdb_species": "s__Brachybacterium sp014897705", "ani": 83.6444, "matched_fragments": 1050, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "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_002332425.1", "gtdb_species": "s__Brachybacterium alimentarium", "ani": 83.5212, "matched_fragments": 987, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.24", "min_intra_species_ani": "99.17", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_000023405.1", "gtdb_species": "s__Brachybacterium faecium", "ani": 83.2969, "matched_fragments": 892, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "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_003994255.1", "gtdb_species": "s__Brachybacterium paraconglomeratum", "ani": 83.2544, "matched_fragments": 873, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.80", "min_intra_species_ani": "96.03", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002407185.1", "gtdb_species": "s__Brachybacterium vulturis", "ani": 83.215, "matched_fragments": 877, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "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_003711805.1", "gtdb_species": "s__Brachybacterium intestinipullorum", "ani": 82.958, "matched_fragments": 915, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.17", "min_intra_species_ani": "99.17", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003347015.1", "gtdb_species": "s__Brachybacterium sp003347015", "ani": 82.8969, "matched_fragments": 872, "total_fragments": 1542, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.176, "cell_length": 0.027, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 30.638, "optimum_ph": 7.25, "genome_size": 3371717.991, "gc_content": 72.133, "coding_genes": 3207.666, "rRNA16S_genes": 3.0, "tRNA_genes": 50.0, "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": 0.333, "coccus_cell_shape": 0.5, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.166, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Brachybacterium", "fresconis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }