{ "type": "genome", "identifier": "GCF_002970975.1", "organism": "Microbacterium halophytorum", "title": "Microbacterium halophytorum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Xinjiang Normal University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002970975.1", "bioproject": "PRJNA224116", "biosample": "SAMN08278568", "wgs_master": "PNFA00000000.1", "refseq_category": "reference genome", "taxid": "2067568", "species_taxid": "2067568", "organism_name": "Microbacterium halophytorum", "infraspecific_name": "strain=YJYP 303", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/06", "asm_name": "ASM297097v1", "asm_submitter": "Xinjiang Normal University", "gbrs_paired_asm": "GCA_002970975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/970/975/GCF_002970975.1_ASM297097v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3331659", "genome_size_ungapped": "3331629", "gc_percent": "70.500000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "23", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002970975.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "2981", "protein_coding_gene_count": "2904", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-06", "dateModified": "2018-03-06", "datePublished": "2018-03-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Microbacterium halophytorum" ], "sample_taxid": [ "2067568" ], "sample_host_organism": [ "Kalidium foliatum" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.888 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)": "3331659", "Number of Sequences": "20", "Longest Sequences (bp)": "627709", "N50 (bp)": "276772", "Gap Ratio (%)": "0.000900", "GCcontent (%)": "70.7", "Number of CDSs": "2954", "Average Protein Length": "341.5", "Coding Ratio (%)": "90.8", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microbacterium halophytorum", "strain": "strain=YJYP 303", "accession": "GCA_002970975.1", "taxid": 2067568, "species_taxid": 2067568, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1101, "total_fragments": 1102, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Microbacterium halotolerans", "strain": "strain=YIM 70130", "accession": "GCA_003569805.1", "taxid": 246613, "species_taxid": 246613, "relation_to_type": "type", "validated": true, "ani": 82.1216, "matched_fragments": 619, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sediminis", "strain": "strain=YLB-01", "accession": "GCA_004564075.1", "taxid": 904291, "species_taxid": 904291, "relation_to_type": "type", "validated": true, "ani": 81.0165, "matched_fragments": 514, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sediminis", "strain": "strain=YLB-01", "accession": "GCA_001689915.1", "taxid": 904291, "species_taxid": 904291, "relation_to_type": "type", "validated": true, "ani": 81.0053, "matched_fragments": 504, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sediminis", "strain": "strain=YLB-01", "accession": "GCA_002741995.1", "taxid": 904291, "species_taxid": 904291, "relation_to_type": "type", "validated": true, "ani": 80.9846, "matched_fragments": 506, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sorbitolivorans", "strain": "strain=CGMCC 1.15228", "accession": "GCA_014641475.1", "taxid": 1867410, "species_taxid": 1867410, "relation_to_type": "type", "validated": true, "ani": 80.6929, "matched_fragments": 498, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium sorbitolivorans", "strain": "strain=CGMCC 1.15228", "accession": "GCA_003327285.1", "taxid": 1867410, "species_taxid": 1867410, "relation_to_type": "type", "validated": true, "ani": 80.6506, "matched_fragments": 498, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium excoecariae", "strain": "strain=CBS5P-1", "accession": "GCA_011326725.1", "taxid": 2715210, "species_taxid": 2715210, "relation_to_type": "type", "validated": true, "ani": 80.3006, "matched_fragments": 491, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium oryzae", "strain": "strain=MB-10", "accession": "GCA_009735645.1", "taxid": 743009, "species_taxid": 743009, "relation_to_type": "type", "validated": true, "ani": 80.1285, "matched_fragments": 518, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium album", "strain": "strain=CGMCC 1.15794", "accession": "GCA_014643695.1", "taxid": 2053191, "species_taxid": 2053191, "relation_to_type": "type", "validated": true, "ani": 79.9912, "matched_fragments": 448, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium marinilacus", "strain": "strain=YM11-607", "accession": "GCA_019753765.1", "taxid": 415209, "species_taxid": 415209, "relation_to_type": "type", "validated": true, "ani": 79.9506, "matched_fragments": 503, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium stercoris", "strain": "strain=NEAU-LLB", "accession": "GCA_017592545.1", "taxid": 2820289, "species_taxid": 2820289, "relation_to_type": "type", "validated": true, "ani": 79.9285, "matched_fragments": 474, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium nanhaiense", "strain": "strain=CGMCC 4.7181", "accession": "GCA_014646015.1", "taxid": 1301026, "species_taxid": 1301026, "relation_to_type": "type", "validated": true, "ani": 79.9218, "matched_fragments": 497, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium commune", "strain": "strain=Re1", "accession": "GCA_014836945.1", "taxid": 2762219, "species_taxid": 2762219, "relation_to_type": "type", "validated": true, "ani": 79.386, "matched_fragments": 414, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium hominis", "strain": "strain=LCDC 84-0209", "accession": "GCA_001553805.1", "taxid": 162426, "species_taxid": 162426, "relation_to_type": "type", "validated": true, "ani": 79.0899, "matched_fragments": 422, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium bovistercoris", "strain": "strain=NEAU-LLE", "accession": "GCA_003387575.1", "taxid": 2293570, "species_taxid": 2293570, "relation_to_type": "type", "validated": true, "ani": 79.0899, "matched_fragments": 437, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbacterium gallinarum", "strain": "strain=Sa1CUA4", "accession": "GCA_014837165.1", "taxid": 2762209, "species_taxid": 2762209, "relation_to_type": "type", "validated": true, "ani": 79.0859, "matched_fragments": 438, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Agromyces luteolus", "strain": "strain=JCM 11431", "accession": "GCA_009729855.1", "taxid": 88373, "species_taxid": 88373, "relation_to_type": "type", "validated": true, "ani": 78.2028, "matched_fragments": 441, "total_fragments": 1102, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002970975.1", "gtdb_species": "s__Microbacterium halophytorum", "ani": 100.0, "matched_fragments": 1101, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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": "conclusive" }, { "accession": "GCF_900163665.1", "gtdb_species": "s__Microbacterium sp900163665", "ani": 82.1922, "matched_fragments": 635, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003569805.1", "gtdb_species": "s__Microbacterium halotolerans", "ani": 82.1133, "matched_fragments": 620, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_004564075.1", "gtdb_species": "s__Microbacterium sediminis", "ani": 81.074, "matched_fragments": 508, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003327285.1", "gtdb_species": "s__Microbacterium sorbitolivorans", "ani": 80.6881, "matched_fragments": 495, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_016805985.1", "gtdb_species": "s__Microbacterium sp016805985", "ani": 80.5023, "matched_fragments": 504, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_001426925.1", "gtdb_species": "s__Microbacterium sp001426925", "ani": 80.4657, "matched_fragments": 501, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_015235415.1", "gtdb_species": "s__Microbacterium paludicola_A", "ani": 80.3438, "matched_fragments": 490, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_011326725.1", "gtdb_species": "s__Microbacterium excoecariae", "ani": 80.3292, "matched_fragments": 489, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.69", "min_intra_species_ani": "95.69", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009735645.1", "gtdb_species": "s__Microbacterium oryzae", "ani": 80.1568, "matched_fragments": 515, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_014643695.1", "gtdb_species": "s__Microbacterium album", "ani": 80.0637, "matched_fragments": 442, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_014646015.1", "gtdb_species": "s__Microbacterium nanhaiense", "ani": 79.9053, "matched_fragments": 498, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_001314225.1", "gtdb_species": "s__Microbacterium sp001314225", "ani": 79.4163, "matched_fragments": 484, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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_004362195.1", "gtdb_species": "s__Microbacterium sp004362195", "ani": 78.8683, "matched_fragments": 413, "total_fragments": 1102, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium", "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": -0.344, "cell_length": -0.025, "doubling_h": null, "growth_tmp": 28.643, "optimum_tmp": 29.019, "optimum_ph": 7.341, "genome_size": 3469503.118, "gc_content": 69.764, "coding_genes": 3206.916, "rRNA16S_genes": 1.75, "tRNA_genes": 50.166, "gram_stain": 1.0, "sporulation": 0.111, "motility": 0.289, "range_salinity": 1.0, "facultative_respiration": 0.012, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.987, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.977, "coccus_cell_shape": 0.022, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Microbacterium", "halophytorum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }