{ "type": "genome", "identifier": "GCF_016106015.1", "organism": "Roseomonas rubea", "title": "Roseomonas rubea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Mokwon University, Korea", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016106015.1", "bioproject": "PRJNA224116", "biosample": "SAMN15375089", "wgs_master": "JACADQ000000000.1", "refseq_category": "reference genome", "taxid": "2748666", "species_taxid": "2748666", "organism_name": "Roseomonas rubea", "infraspecific_name": "strain=MO17", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/12/17", "asm_name": "ASM1610601v1", "asm_submitter": "Mokwon University, Korea", "gbrs_paired_asm": "GCA_016106015.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/106/015/GCF_016106015.1_ASM1610601v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5006782", "genome_size_ungapped": "5006782", "gc_percent": "71.000000", "replicon_count": "0", "scaffold_count": "774", "contig_count": "774", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016106015.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "5223", "protein_coding_gene_count": "4953", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-12-17", "dateModified": "2020-12-17", "datePublished": "2020-12-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Roseomonas rubea" ], "sample_taxid": [ "2748666" ], "sample_host_organism": [ "paddy soil" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "1.348 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5006782", "Number of Sequences": "774", "Longest Sequences (bp)": "75469", "N50 (bp)": "11753", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "71.2", "Number of CDSs": "4250", "Average Protein Length": "306.4", "Coding Ratio (%)": "78.0", "Number of rRNAs": "3", "Number of tRNAs": "55", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseomonas rubea", "strain": "strain=MO17", "accession": "GCA_016106015.1", "taxid": 2748666, "species_taxid": 2748666, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1289, "total_fragments": 1302, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseomonas alkaliterrae", "strain": "strain=DSM 25895", "accession": "GCA_014199195.1", "taxid": 1452450, "species_taxid": 1452450, "relation_to_type": "type", "validated": true, "ani": 84.3867, "matched_fragments": 906, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas oryzicola", "strain": "strain=KCTC 22478", "accession": "GCA_012163135.1", "taxid": 535904, "species_taxid": 535904, "relation_to_type": "type", "validated": true, "ani": 84.3694, "matched_fragments": 980, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas lacus", "strain": "strain=CGMCC 1.3617", "accession": "GCA_014644535.1", "taxid": 287609, "species_taxid": 287609, "relation_to_type": "type", "validated": true, "ani": 82.1808, "matched_fragments": 939, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas hellenica", "strain": "strain=LMG 31523", "accession": "GCA_018129085.1", "taxid": 2687306, "species_taxid": 2687306, "relation_to_type": "type", "validated": true, "ani": 79.6861, "matched_fragments": 694, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Falsiroseomonas tokyonensis", "strain": "strain=K-20", "accession": "GCA_019024325.1", "taxid": 430521, "species_taxid": 430521, "relation_to_type": "type", "validated": true, "ani": 79.1941, "matched_fragments": 713, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Siccirubricoccus deserti", "strain": "strain=SYSU D8009", "accession": "GCA_014283215.1", "taxid": 2013562, "species_taxid": 2013562, "relation_to_type": "type", "validated": true, "ani": 79.0129, "matched_fragments": 616, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Siccirubricoccus deserti", "strain": "strain=CGMCC 1.15936", "accession": "GCA_014644195.1", "taxid": 2013562, "species_taxid": 2013562, "relation_to_type": "type", "validated": true, "ani": 78.9797, "matched_fragments": 623, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseococcus pinisoli", "strain": "strain=XZZS9", "accession": "GCA_018413645.1", "taxid": 2835040, "species_taxid": 2835040, "relation_to_type": "type", "validated": true, "ani": 78.7514, "matched_fragments": 540, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovarius lipocyclicus", "strain": "strain=CCUG 44693", "accession": "GCA_009900765.1", "taxid": 268410, "species_taxid": 268410, "relation_to_type": "type", "validated": true, "ani": 78.6876, "matched_fragments": 519, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas deserti", "strain": "strain=M3", "accession": "GCA_001982615.1", "taxid": 1817963, "species_taxid": 1817963, "relation_to_type": "type", "validated": true, "ani": 78.56, "matched_fragments": 556, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas haemaphysalidis", "strain": "strain=546", "accession": "GCA_017355405.1", "taxid": 2768162, "species_taxid": 2768162, "relation_to_type": "type", "validated": true, "ani": 78.4379, "matched_fragments": 464, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas marmotae", "strain": "strain=1318", "accession": "GCA_017654485.1", "taxid": 2768161, "species_taxid": 2768161, "relation_to_type": "type", "validated": true, "ani": 78.3692, "matched_fragments": 447, "total_fragments": 1302, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016106015.1", "gtdb_species": "s__Roseomonas_B 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84.667, "matched_fragments": 912, "total_fragments": 1302, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B", "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_005222755.1", "gtdb_species": "s__Roseomonas_B sp005222755", "ani": 84.4176, "matched_fragments": 1006, "total_fragments": 1302, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B", "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_014199195.1", "gtdb_species": "s__Roseomonas_B alkaliterrae", "ani": 84.3605, "matched_fragments": 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1302, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B", "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_018129065.1", "gtdb_species": "s__Roseomonas_B soli", "ani": 83.938, "matched_fragments": 911, "total_fragments": 1302, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B", "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_001464375.1", "gtdb_species": "s__Roseomonas_B sp001464375", "ani": 83.5953, "matched_fragments": 881, "total_fragments": 1302, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B", "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": -0.121, "cell_length": 0.031, "doubling_h": null, "growth_tmp": 29.928, "optimum_tmp": 29.85, "optimum_ph": 7.031, "genome_size": 5614233.625, "gc_content": 66.545, "coding_genes": 4734.0, "rRNA16S_genes": 5.0, "tRNA_genes": 59.0, "gram_stain": 0.0, "sporulation": 0.25, "motility": 0.3, "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": 0.222, "coccus_cell_shape": 0.444, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.333, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Roseomonas", "rubea" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }