{ "type": "genome", "identifier": "GCF_016026595.1", "organism": "Brevibacterium casei", "title": "Brevibacterium casei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US Food and Drug Administration", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016026595.1", "bioproject": "PRJNA224116", "biosample": "SAMN13450466", "wgs_master": "na", "refseq_category": "na", "taxid": "33889", "species_taxid": "33889", "organism_name": "Brevibacterium casei", "infraspecific_name": "strain=FDAARGOS_936", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/12/14", "asm_name": "ASM1602659v1", "asm_submitter": "US Food and Drug Administration", "gbrs_paired_asm": "GCA_016026595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/026/595/GCF_016026595.1_ASM1602659v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3866591", "genome_size_ungapped": "3866591", "gc_percent": "68.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-15", "total_gene_count": "3511", "protein_coding_gene_count": "3420", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-12-14", "dateModified": "2020-12-14", "datePublished": "2020-12-14", "_annotation": { "sample_count": 1, "sample_organism": [ "Brevibacterium casei" ], "sample_taxid": [ "33889" ], "sample_host_organism": [ "missing" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown", "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "Not applicable" ], "sample_host_location_id": [], "data_size": "1.041 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)": "3866591", "Number of Sequences": "1", "Longest Sequences (bp)": "3866591", "N50 (bp)": "3866591", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.0", "Number of CDSs": "3527", "Average Protein Length": "329.8", "Coding Ratio (%)": "90.3", "Number of rRNAs": "6", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Brevibacterium casei", "strain": "strain=FDAARGOS_936", "accession": "GCA_016026595.1", "taxid": 33889, "species_taxid": 33889, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1288, "total_fragments": 1288, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Brevibacterium casei", "strain": "strain=CIP 102111", "accession": "GCA_900169275.1", "taxid": 33889, "species_taxid": 33889, "relation_to_type": "type", "validated": true, "ani": 99.9863, "matched_fragments": 1268, "total_fragments": 1288, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Brevibacterium atlanticum", "strain": "strain=WO024", "accession": "GCA_011617245.1", "taxid": 2697563, "species_taxid": 2697563, "relation_to_type": "type", "validated": true, "ani": 82.1185, "matched_fragments": 801, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium oceani", "strain": "strain=BBH7", "accession": "GCA_013623835.1", "taxid": 358099, "species_taxid": 358099, "relation_to_type": "type", "validated": true, "ani": 81.9887, "matched_fragments": 828, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium pigmentatum", "strain": "strain=YB235", "accession": "GCA_011617465.1", "taxid": 1496080, "species_taxid": 1496080, "relation_to_type": "type", "validated": true, "ani": 81.5975, "matched_fragments": 778, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium renqingii", "strain": "strain=REN4", "accession": "GCA_017808105.1", "taxid": 2776916, "species_taxid": 2776916, "relation_to_type": "type", "validated": true, "ani": 81.5752, "matched_fragments": 761, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium limosum", "strain": "strain=o2", "accession": "GCA_011617705.1", "taxid": 2697565, "species_taxid": 2697565, "relation_to_type": "type", "validated": true, "ani": 81.4649, "matched_fragments": 788, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium permense", "strain": "strain=VKM Ac-2280", "accession": "GCA_013280495.1", "taxid": 234834, "species_taxid": 234834, "relation_to_type": "type", "validated": true, "ani": 81.4372, "matched_fragments": 755, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium linens", "strain": "strain=ATCC 9172", "accession": "GCA_008868375.1", "taxid": 1703, "species_taxid": 1703, "relation_to_type": "suspected-type", "validated": true, "ani": 81.3687, "matched_fragments": 771, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium sediminis", "strain": "strain=FXJ8.269", "accession": "GCA_013623905.1", "taxid": 1857024, "species_taxid": 1857024, "relation_to_type": "type", "validated": true, "ani": 81.3441, "matched_fragments": 797, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium sediminis", "strain": "strain=CGMCC 1.15472", "accession": "GCA_014643055.1", "taxid": 1857024, "species_taxid": 1857024, "relation_to_type": "type", "validated": true, "ani": 81.3238, "matched_fragments": 799, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium iodinum", "strain": "strain=ATCC 49514", "accession": "GCA_900169265.1", "taxid": 31943, "species_taxid": 31943, "relation_to_type": "type", "validated": true, "ani": 81.2279, "matched_fragments": 728, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium zhoupengii", "strain": "strain=HY170", "accession": "GCA_021117425.1", "taxid": 2898795, "species_taxid": 2898795, "relation_to_type": "type", "validated": true, "ani": 80.3911, "matched_fragments": 737, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium antiquum", "strain": "strain=DSM 21545", "accession": "GCA_016107655.1", "taxid": 234835, "species_taxid": 234835, "relation_to_type": "type", "validated": true, "ani": 80.3499, "matched_fragments": 723, "total_fragments": 1288, "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": 76.9051, "matched_fragments": 203, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia merdavium", "strain": "strain=Sa2CUA9", "accession": "GCA_014836755.1", "taxid": 2762227, "species_taxid": 2762227, "relation_to_type": "type", "validated": true, "ani": 76.7788, "matched_fragments": 216, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oerskovia douganii", "strain": "strain=Sa1BUA8", "accession": "GCA_015142735.1", "taxid": 2762210, "species_taxid": 2762210, "relation_to_type": "type", "validated": true, "ani": 76.753, "matched_fragments": 225, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces cavernae", "strain": "strain=SYSU K20354", "accession": "GCA_021044935.1", "taxid": 2898659, "species_taxid": 2898659, "relation_to_type": "type", "validated": true, "ani": 76.5701, "matched_fragments": 226, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=LMG 11597", "accession": "GCA_000741775.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 76.1956, "matched_fragments": 50, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=DSM 20096", "accession": "GCA_000426405.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 76.1276, "matched_fragments": 50, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bifidobacterium subtile", "strain": "strain=DSM 20096", "accession": "GCA_000771185.1", "taxid": 77635, "species_taxid": 77635, "relation_to_type": "type", "validated": true, "ani": 76.0297, "matched_fragments": 51, "total_fragments": 1288, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900169275.1", "gtdb_species": "s__Brevibacterium casei", "ani": 99.9863, "matched_fragments": 1268, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.23", "min_intra_species_ani": "97.33", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 17, "status": "conclusive" }, { "accession": "GCF_006489205.1", "gtdb_species": "s__Brevibacterium sp006489205", "ani": 87.5312, "matched_fragments": 1066, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018137945.1", "gtdb_species": "s__Brevibacterium sp018137945", "ani": 86.827, "matched_fragments": 1059, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.80", "min_intra_species_ani": "97.80", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003315415.1", "gtdb_species": "s__Brevibacterium celere_A", "ani": 82.6561, "matched_fragments": 801, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "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_011617245.1", "gtdb_species": "s__Brevibacterium sp011617245", "ani": 82.1132, "matched_fragments": 800, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "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_013623835.1", "gtdb_species": "s__Brevibacterium oceani", "ani": 81.9887, "matched_fragments": 828, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.48", "min_intra_species_ani": "96.48", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_017808105.1", "gtdb_species": "s__Brevibacterium renqingii", "ani": 81.6039, "matched_fragments": 758, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "98.54", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_011617465.1", "gtdb_species": "s__Brevibacterium sp011617465", "ani": 81.579, "matched_fragments": 778, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "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_012844365.1", "gtdb_species": "s__Brevibacterium sp012844365", "ani": 81.4968, "matched_fragments": 821, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "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_011617705.1", "gtdb_species": "s__Brevibacterium sp011617705", "ani": 81.4424, "matched_fragments": 785, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.55", "min_intra_species_ani": "96.55", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900169165.1", "gtdb_species": "s__Brevibacterium linens", "ani": 81.4048, "matched_fragments": 768, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.12", "min_intra_species_ani": "96.02", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.82", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_013623905.1", "gtdb_species": "s__Brevibacterium sediminis", "ani": 81.3356, "matched_fragments": 798, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "97.49", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_015142735.1", "gtdb_species": "s__Oerskovia sp015142735", "ani": 76.7618, "matched_fragments": 223, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Oerskovia", "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_000719775.1", "gtdb_species": "s__Streptomyces sp000719775", "ani": 75.9866, "matched_fragments": 187, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces", "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_013360825.1", "gtdb_species": "s__WSZJ01 sp013360825", "ani": 74.8484, "matched_fragments": 53, "total_fragments": 1288, "gtdb_taxonomy": "d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__WSZJ01;g__WSZJ01", "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": -0.143, "cell_length": 0.151, "doubling_h": null, "growth_tmp": 32.0, "optimum_tmp": 31.167, "optimum_ph": 7.911, "genome_size": 3783468.333, "gc_content": 68.12, "coding_genes": 3606.375, "rRNA16S_genes": 4.0, "tRNA_genes": 48.5, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.1, "range_salinity": null, "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": 0.833, "coccus_cell_shape": 0.111, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.055, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Brevibacterium", "casei" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }