{ "type": "genome", "identifier": "GCF_003148845.1", "organism": "Mucilaginibacter oryzae", "title": "Mucilaginibacter oryzae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003148845.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660888", "wgs_master": "QGHA00000000.1", "refseq_category": "reference genome", "taxid": "468058", "species_taxid": "468058", "organism_name": "Mucilaginibacter oryzae", "infraspecific_name": "strain=DSM 19975", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/05/22", "asm_name": "ASM314884v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_003148845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/148/845/GCF_003148845.1_ASM314884v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5939202", "genome_size_ungapped": "5938162", "gc_percent": "44.000000", "replicon_count": "0", "scaffold_count": "41", "contig_count": "41", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003148845.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "5089", "protein_coding_gene_count": "5000", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-05-22", "dateModified": "2018-05-22", "datePublished": "2018-05-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Mucilaginibacter oryzae" ], "sample_taxid": [ "468058" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jinju" ], "sample_host_location_id": [], "data_size": "1.682 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)": "5939202", "Number of Sequences": "41", "Longest Sequences (bp)": "1259500", "N50 (bp)": "514626", "Gap Ratio (%)": "0.017511", "GCcontent (%)": "44.2", "Number of CDSs": "4914", "Average Protein Length": "345.9", "Coding Ratio (%)": "85.9", "Number of rRNAs": "4", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mucilaginibacter oryzae", "strain": "strain=DSM 19975", "accession": "GCA_003148845.1", "taxid": 468058, "species_taxid": 468058, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1956, "total_fragments": 1957, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mucilaginibacter celer", "strain": "strain=HYN0043", "accession": "GCA_003576455.2", "taxid": 2305508, "species_taxid": 2305508, "relation_to_type": "type", "validated": true, "ani": 84.2513, "matched_fragments": 1371, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter rubeus", "strain": "strain=CGMCC 1.15913", "accession": "GCA_014643835.1", "taxid": 2027860, "species_taxid": 2027860, "relation_to_type": "suspected-type", "validated": true, "ani": 81.1432, "matched_fragments": 1056, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter gossypii", "strain": "strain=Gh-67", "accession": "GCA_900100945.1", "taxid": 551996, "species_taxid": 551996, "relation_to_type": "type", "validated": true, "ani": 81.0753, "matched_fragments": 1044, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter endophyticus", "strain": "strain=RS1", "accession": "GCA_003351025.1", "taxid": 2675003, "species_taxid": 2675003, "relation_to_type": "type", "validated": true, "ani": 81.0733, "matched_fragments": 1108, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter kameinonensis", "strain": "strain=SCK", "accession": "GCA_003675385.1", "taxid": 452286, "species_taxid": 452286, "relation_to_type": "type", "validated": true, "ani": 80.9762, "matched_fragments": 1087, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter gossypiicola", "strain": "strain=Gh-48", "accession": "GCA_900110105.1", "taxid": 551995, "species_taxid": 551995, "relation_to_type": "type", "validated": true, "ani": 80.9717, "matched_fragments": 1081, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter pineti", "strain": "strain=47C3B", "accession": "GCA_900101875.1", "taxid": 1391627, "species_taxid": 1391627, "relation_to_type": "type", "validated": true, "ani": 78.3725, "matched_fragments": 636, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter phyllosphaerae", "strain": "strain=PP-F2FG21", "accession": "GCA_004378255.1", "taxid": 1812349, "species_taxid": 1812349, "relation_to_type": "type", "validated": true, "ani": 77.9147, "matched_fragments": 389, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter conchicola", "strain": "strain=MYSH2", "accession": "GCA_003432115.1", "taxid": 2303333, "species_taxid": 2303333, "relation_to_type": "type", "validated": true, "ani": 77.7957, "matched_fragments": 370, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter pallidiroseus", "strain": "strain=dk17", "accession": "GCA_007846085.1", "taxid": 2599295, "species_taxid": 2599295, "relation_to_type": "type", "validated": true, "ani": 77.7823, "matched_fragments": 282, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter achroorhodeus", "strain": "strain=MJ1a", "accession": "GCA_007846095.1", "taxid": 2599294, "species_taxid": 2599294, "relation_to_type": "type", "validated": true, "ani": 77.6565, "matched_fragments": 307, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter gilvus", "strain": "strain=F01003", "accession": "GCA_004054195.1", "taxid": 2305909, "species_taxid": 2305909, "relation_to_type": "type", "validated": true, "ani": 77.4928, "matched_fragments": 383, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter paludis", "strain": "strain=DSM 18603", "accession": "GCA_000166195.3", "taxid": 423351, "species_taxid": 423351, "relation_to_type": "type", "validated": true, "ani": 77.1249, "matched_fragments": 309, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter polaris", "strain": "strain=RP-3-22", "accession": "GCA_005116505.1", "taxid": 2571273, "species_taxid": 2571273, "relation_to_type": "type", "validated": true, "ani": 76.2849, "matched_fragments": 55, "total_fragments": 1957, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003148845.1", "gtdb_species": "s__Mucilaginibacter oryzae", "ani": 100.0, "matched_fragments": 1956, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_003576455.2", "gtdb_species": "s__Mucilaginibacter celer", "ani": 84.2677, "matched_fragments": 1367, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_014643835.1", "gtdb_species": "s__Mucilaginibacter rubeus", "ani": 81.1331, "matched_fragments": 1058, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.62", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003351025.1", "gtdb_species": "s__Mucilaginibacter endophyticus", "ani": 81.0757, "matched_fragments": 1109, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_900100945.1", "gtdb_species": "s__Mucilaginibacter gossypii", "ani": 81.06, "matched_fragments": 1047, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.19", "min_intra_species_ani": "95.83", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.84", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_003664165.1", "gtdb_species": "s__Mucilaginibacter sp003664165", "ani": 80.9917, "matched_fragments": 1111, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_900110105.1", "gtdb_species": "s__Mucilaginibacter gossypiicola", "ani": 80.9819, "matched_fragments": 1079, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_003675385.1", "gtdb_species": "s__Mucilaginibacter kameinonensis", "ani": 80.9733, "matched_fragments": 1088, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.21", "min_intra_species_ani": "95.21", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003208075.1", "gtdb_species": "s__Mucilaginibacter sp003208075", "ani": 80.8992, "matched_fragments": 1075, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_007846085.1", "gtdb_species": "s__Mucilaginibacter sp007846085", "ani": 77.7712, "matched_fragments": 283, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_000166195.2", "gtdb_species": "s__Mucilaginibacter paludis", "ani": 77.1207, "matched_fragments": 312, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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_018266935.1", "gtdb_species": "s__Mucilaginibacter sp018266935", "ani": 76.7038, "matched_fragments": 162, "total_fragments": 1957, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter", "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": -0.188, "cell_length": 0.332, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 27.5, "optimum_ph": 6.0, "genome_size": 5939202.0, "gc_content": 43.045, "coding_genes": 5407.0, "rRNA16S_genes": 2.0, "tRNA_genes": 47.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mucilaginibacter", "oryzae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }