{ "type": "genome", "identifier": "GCF_013280495.1", "organism": "Brevibacterium permense", "title": "Brevibacterium permense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute Of Oceanography,MNR", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013280495.1", "bioproject": "PRJNA224116", "biosample": "SAMN14820126", "wgs_master": "JABSSX000000000.1", "refseq_category": "reference genome", "taxid": "234834", "species_taxid": "234834", "organism_name": "Brevibacterium permense", "infraspecific_name": "strain=VKM Ac-2280", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/05", "asm_name": "ASM1328049v1", "asm_submitter": "Third Institute Of Oceanography,MNR", "gbrs_paired_asm": "GCA_013280495.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/280/495/GCF_013280495.1_ASM1328049v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3702760", "genome_size_ungapped": "3702760", "gc_percent": "64.500000", "replicon_count": "0", "scaffold_count": "40", "contig_count": "40", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013280495.1-RS_2024_04_30", "annotation_date": "2024-04-30", "total_gene_count": "3375", "protein_coding_gene_count": "3282", "non_coding_gene_count": "55", "pubmed_id": "15198034" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-05", "dateModified": "2020-06-05", "datePublished": "2020-06-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Brevibacterium permense" ], "sample_taxid": [ "234834" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Russia: Perm region" ], "sample_host_location_id": [], "data_size": "1.025 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)": "3702760", "Number of Sequences": "40", "Longest Sequences (bp)": "607888", "N50 (bp)": "365608", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.5", "Number of CDSs": "3371", "Average Protein Length": "325.7", "Coding Ratio (%)": "89.0", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1211, "total_fragments": 1213, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Brevibacterium iodinum", "strain": "strain=ATCC 49514", "accession": "GCA_900169265.1", "taxid": 31943, "species_taxid": 31943, "relation_to_type": "type", "validated": true, "ani": 94.7796, "matched_fragments": 1000, "total_fragments": 1213, "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": 94.3798, "matched_fragments": 1054, "total_fragments": 1213, "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": 94.3655, "matched_fragments": 1055, "total_fragments": 1213, "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": 91.6039, "matched_fragments": 995, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium linens", "strain": "strain=ATCC 9172", "accession": "GCA_900169165.1", "taxid": 1703, "species_taxid": 1703, "relation_to_type": "suspected-type", "validated": true, "ani": 91.5819, "matched_fragments": 1007, "total_fragments": 1213, "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": 91.5285, "matched_fragments": 1080, "total_fragments": 1213, "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": 81.1202, "matched_fragments": 795, "total_fragments": 1213, "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": 80.9658, "matched_fragments": 782, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium gallinarum", "strain": "strain=Re57", "accession": "GCA_014836885.1", "taxid": 2762220, "species_taxid": 2762220, "relation_to_type": "type", "validated": true, "ani": 78.7967, "matched_fragments": 365, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Brevibacterium daeguense", "strain": "strain=DSM 27938", "accession": "GCA_021729135.1", "taxid": 909936, "species_taxid": 909936, "relation_to_type": "type", "validated": true, "ani": 78.0036, "matched_fragments": 310, "total_fragments": 1213, "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": 76.7058, "matched_fragments": 122, "total_fragments": 1213, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013280495.1", "gtdb_species": "s__Brevibacterium permense", "ani": 100.0, "matched_fragments": 1211, "total_fragments": 1213, "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": "conclusive" }, { "accession": "GCF_900169265.1", "gtdb_species": "s__Brevibacterium iodinum", "ani": 94.8, "matched_fragments": 999, "total_fragments": 1213, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium", "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": "-" }, { "accession": "GCF_013623905.1", "gtdb_species": "s__Brevibacterium sediminis", "ani": 94.3655, "matched_fragments": 1055, "total_fragments": 1213, "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_900169165.1", "gtdb_species": "s__Brevibacterium linens", "ani": 91.5748, "matched_fragments": 1008, "total_fragments": 1213, "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_011617465.1", "gtdb_species": "s__Brevibacterium sp011617465", "ani": 91.5311, "matched_fragments": 1079, "total_fragments": 1213, "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": 91.2186, "matched_fragments": 1053, "total_fragments": 1213, "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_900105315.1", "gtdb_species": "s__Brevibacterium siliguriense", "ani": 90.1158, "matched_fragments": 1015, "total_fragments": 1213, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.143, "cell_length": 0.151, "doubling_h": null, "growth_tmp": 29.0, "optimum_tmp": 30.436, "optimum_ph": 7.911, "genome_size": 3680194.756, "gc_content": 64.593, "coding_genes": 3606.375, "rRNA16S_genes": 4.0, "tRNA_genes": 48.5, "gram_stain": 1.0, "sporulation": 0.052, "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", "permense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }