{ "type": "genome", "identifier": "GCF_021729035.1", "organism": "Microbulbifer sediminum", "title": "Microbulbifer sediminum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Second Institute of Oceanography, Ministry of Natural Resources", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021729035.1", "bioproject": "PRJNA224116", "biosample": "SAMN24045730", "wgs_master": "JAJSAP000000000.1", "refseq_category": "reference genome", "taxid": "2904250", "species_taxid": "2904250", "organism_name": "Microbulbifer sediminum", "infraspecific_name": "strain=TT37", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/01/30", "asm_name": "ASM2172903v1", "asm_submitter": "Second Institute of Oceanography, Ministry of Natural Resources", "gbrs_paired_asm": "GCA_021729035.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/729/035/GCF_021729035.1_ASM2172903v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3854156", "genome_size_ungapped": "3853956", "gc_percent": "61.000000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "15", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021729035.1-RS_2024_08_08", "annotation_date": "2024-08-08", "total_gene_count": "3381", "protein_coding_gene_count": "3321", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-01-30", "dateModified": "2022-01-30", "datePublished": "2022-01-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Microbulbifer sediminum" ], "sample_taxid": [ "2904250" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Zhoushan" ], "sample_host_location_id": [], "data_size": "1.087 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)": "3854156", "Number of Sequences": "15", "Longest Sequences (bp)": "668221", "N50 (bp)": "456599", "Gap Ratio (%)": "0.005189", "GCcontent (%)": "60.9", "Number of CDSs": "3360", "Average Protein Length": "335.4", "Coding Ratio (%)": "87.7", "Number of rRNAs": "3", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Microbulbifer yueqingensis", "strain": "strain=CGMCC 1.10658", "accession": "GCA_900100355.1", "taxid": 658219, "species_taxid": 658219, "relation_to_type": "type", "validated": true, "ani": 83.026, "matched_fragments": 843, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer taiwanensis", "strain": "strain=LMG 26125", "accession": "GCA_014904815.1", "taxid": 986746, "species_taxid": 986746, "relation_to_type": "type", "validated": true, "ani": 80.4355, "matched_fragments": 659, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer marinus", "strain": "strain=CGMCC 1.10657", "accession": "GCA_900107725.1", "taxid": 658218, "species_taxid": 658218, "relation_to_type": "type", "validated": true, "ani": 80.2788, "matched_fragments": 634, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer donghaiensis", "strain": "strain=CGMCC 1.7063", "accession": "GCA_900129095.1", "taxid": 494016, "species_taxid": 494016, "relation_to_type": "type", "validated": true, "ani": 80.1273, "matched_fragments": 642, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer flavimaris", "strain": "strain=WRN-8", "accession": "GCA_001641755.2", "taxid": 1781068, "species_taxid": 1781068, "relation_to_type": "type", "validated": true, "ani": 80.0387, "matched_fragments": 606, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer aggregans", "strain": "strain=CCB-MM1", "accession": "GCA_001750105.1", "taxid": 1769779, "species_taxid": 1769779, "relation_to_type": "type", "validated": true, "ani": 79.9044, "matched_fragments": 598, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer rhizosphaerae", "strain": "strain=CECT 8799", "accession": "GCA_014191725.1", "taxid": 1562603, "species_taxid": 1562603, "relation_to_type": "type", "validated": true, "ani": 79.8969, "matched_fragments": 586, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer hainanensis", "strain": "strain=NBU-8HK146", "accession": "GCA_014904735.1", "taxid": 2735675, "species_taxid": 2735675, "relation_to_type": "type", "validated": true, "ani": 79.8775, "matched_fragments": 619, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer celer", "strain": "strain=KCTC 12973", "accession": "GCA_020991125.1", "taxid": 435905, "species_taxid": 435905, "relation_to_type": "type", "validated": true, "ani": 79.1077, "matched_fragments": 447, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer elongatus", "strain": "strain=DSM 6810", "accession": "GCA_021165935.1", "taxid": 86173, "species_taxid": 86173, "relation_to_type": "type", "validated": true, "ani": 78.8683, "matched_fragments": 428, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Microbulbifer elongatus", "strain": "strain=DSM 6810", "accession": "GCA_022554105.1", "taxid": 86173, "species_taxid": 86173, "relation_to_type": "type", "validated": true, "ani": 78.7489, "matched_fragments": 440, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_021602585.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 76.6522, "matched_fragments": 148, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_013373935.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 76.5749, "matched_fragments": 146, "total_fragments": 1276, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900100355.1", "gtdb_species": "s__Microbulbifer yueqingensis", "ani": 83.026, "matched_fragments": 843, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_014904815.1", "gtdb_species": "s__Microbulbifer taiwanensis", "ani": 80.4462, "matched_fragments": 657, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_900107725.1", "gtdb_species": "s__Microbulbifer marinus", "ani": 80.2664, "matched_fragments": 635, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_900129095.1", "gtdb_species": "s__Microbulbifer donghaiensis", "ani": 80.1185, "matched_fragments": 643, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_001641755.2", "gtdb_species": "s__Microbulbifer flavimaris", "ani": 80.0294, "matched_fragments": 607, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_014191725.1", "gtdb_species": "s__Microbulbifer rhizosphaerae", "ani": 79.9158, "matched_fragments": 584, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_001750105.1", "gtdb_species": "s__Microbulbifer aggregans", "ani": 79.9036, "matched_fragments": 600, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_014904735.1", "gtdb_species": "s__Microbulbifer hainanensis", "ani": 79.882, "matched_fragments": 618, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_002959965.1", "gtdb_species": "s__Microbulbifer pacificus", "ani": 79.1024, "matched_fragments": 416, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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_009903625.1", "gtdb_species": "s__Microbulbifer sp009903625", "ani": 78.8882, "matched_fragments": 439, "total_fragments": 1276, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer", "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": -0.362, "cell_length": 0.344, "doubling_h": null, "growth_tmp": 31.3, "optimum_tmp": 34.357, "optimum_ph": 7.262, "genome_size": 4107737.857, "gc_content": 56.958, "coding_genes": 3303.166, "rRNA16S_genes": 3.333, "tRNA_genes": 59.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.142, "range_salinity": null, "facultative_respiration": 0.125, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.875, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.857, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.142, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Microbulbifer", "sediminum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }