{ "type": "genome", "identifier": "GCF_017654485.1", "organism": "Roseomonas marmotae", "title": "Roseomonas marmotae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Center for Disease Control and Prevention", "publication": [ {} ], "properties": { "assembly_accession": "GCF_017654485.1", "bioproject": "PRJNA224116", "biosample": "SAMN15936121", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2768161", "species_taxid": "2768161", "organism_name": "Roseomonas marmotae", "infraspecific_name": "strain=1318", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/03/31", "asm_name": "ASM1765448v1", "asm_submitter": "Chinese Center for Disease Control and Prevention", "gbrs_paired_asm": "GCA_017654485.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/017/654/485/GCF_017654485.1_ASM1765448v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4833053", "genome_size_ungapped": "4833053", "gc_percent": "69.000000", "replicon_count": "10", "scaffold_count": "10", "contig_count": "10", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_017654485.1-RS_2024_03_13", "annotation_date": "2024-03-13", "total_gene_count": "4602", "protein_coding_gene_count": "4427", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-03-31", "dateModified": "2021-03-31", "datePublished": "2021-03-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Roseomonas marmotae" ], "sample_taxid": [ "2768161" ], "sample_host_organism": [ "Marmota himalayana" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Qinghai province" ], "sample_host_location_id": [], "data_size": "1.307 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)": "4833053", "Number of Sequences": "10", "Longest Sequences (bp)": "3565232", "N50 (bp)": "3565232", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.8", "Number of CDSs": "4636", "Average Protein Length": "313.5", "Coding Ratio (%)": "90.2", "Number of rRNAs": "15", "Number of tRNAs": "63", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseomonas marmotae", "strain": "strain=1318", "accession": "GCA_017654485.1", "taxid": 2768161, "species_taxid": 2768161, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1606, "total_fragments": 1607, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Roseomonas wenyumeiae", "strain": "strain=Z23", "accession": "GCA_003696345.1", "taxid": 2478470, "species_taxid": 2478470, "relation_to_type": "type", "validated": true, "ani": 86.2782, "matched_fragments": 1192, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas ludipueritiae", "strain": "strain=DSM 14915", "accession": "GCA_014490445.1", "taxid": 198093, "species_taxid": 198093, "relation_to_type": "type", "validated": true, "ani": 86.206, "matched_fragments": 987, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas aerophila", "strain": "strain=NBRC 108923", "accession": "GCA_014490485.1", "taxid": 1224513, "species_taxid": 1224513, "relation_to_type": "type", "validated": true, "ani": 83.0371, "matched_fragments": 953, "total_fragments": 1607, "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": 82.7797, "matched_fragments": 974, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas cervicalis", "strain": "strain=ATCC 49957", "accession": "GCA_000164635.1", "taxid": 204525, "species_taxid": 204525, "relation_to_type": "type", "validated": true, "ani": 81.9285, "matched_fragments": 775, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas rhizosphaerae", "strain": "strain=YW11", "accession": "GCA_002631185.1", "taxid": 1335062, "species_taxid": 1335062, "relation_to_type": "type", "validated": true, "ani": 81.8638, "matched_fragments": 836, "total_fragments": 1607, "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": 78.5359, "matched_fragments": 531, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseomonas rubea", "strain": "strain=MO17", "accession": "GCA_016106015.1", "taxid": 2748666, "species_taxid": 2748666, "relation_to_type": "type", "validated": true, "ani": 78.5248, "matched_fragments": 469, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodovarius crocodyli", "strain": "strain=CCP-6", "accession": "GCA_004005855.1", "taxid": 1979269, "species_taxid": 1979269, "relation_to_type": "type", "validated": true, "ani": 78.2438, "matched_fragments": 552, "total_fragments": 1607, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_017654485.1", "gtdb_species": "s__Roseomonas sp017654485", "ani": 100.0, "matched_fragments": 1606, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.93", "min_intra_species_ani": "99.93", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_003696345.1", "gtdb_species": "s__Roseomonas sp003696345", "ani": 86.3129, "matched_fragments": 1186, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014490445.1", "gtdb_species": "s__Roseomonas ludipueritiae", "ani": 86.2083, "matched_fragments": 987, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas", "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_014490485.1", "gtdb_species": "s__Roseomonas aerophila", "ani": 83.0539, "matched_fragments": 953, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas", "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_017355405.1", "gtdb_species": "s__Roseomonas sp017355405", "ani": 82.7533, "matched_fragments": 974, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas", "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": "GCA_000245075.1", "gtdb_species": "s__Roseomonas sp000245075", "ani": 82.4385, "matched_fragments": 869, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas", "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_000164635.1", "gtdb_species": "s__Roseomonas cervicalis", "ani": 81.9156, "matched_fragments": 776, "total_fragments": 1607, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas", "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", "marmotae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }