{ "type": "genome", "identifier": "GCF_019130055.1", "organism": "Rhodobacter amnigenus", "title": "Rhodobacter amnigenus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Kaohsiung University of Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019130055.1", "bioproject": "PRJNA224116", "biosample": "SAMN19868579", "wgs_master": "JAHSPE000000000.1", "refseq_category": "na", "taxid": "2852097", "species_taxid": "2852097", "organism_name": "Rhodobacter amnigenus", "infraspecific_name": "strain=HSP-20", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/06", "asm_name": "ASM1913005v1", "asm_submitter": "National Kaohsiung University of Science and Technology", "gbrs_paired_asm": "GCA_019130055.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/130/055/GCF_019130055.1_ASM1913005v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4142744", "genome_size_ungapped": "4142744", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-19", "total_gene_count": "4074", "protein_coding_gene_count": "3980", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-06", "dateModified": "2021-07-06", "datePublished": "2021-07-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Rhodobacter amnigenus" ], "sample_taxid": [ "2852097" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Taiwan" ], "sample_host_location_id": [], "data_size": "1.131 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)": "4142744", "Number of Sequences": "37", "Longest Sequences (bp)": "472152", "N50 (bp)": "285898", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.2", "Number of CDSs": "4029", "Average Protein Length": "309.3", "Coding Ratio (%)": "90.2", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_019130055.1", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1362, "total_fragments": 1363, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodobacter amnigenus", "strain": "strain=HSP-20", "accession": "GCA_009908265.2", "taxid": 2852097, "species_taxid": 2852097, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1362, "total_fragments": 1363, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Rhodobacter ruber", "strain": "strain=CCP-1", "accession": "GCA_009908315.1", "taxid": 1985673, "species_taxid": 1985673, "relation_to_type": "type", "validated": true, "ani": 84.5495, "matched_fragments": 875, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter straminiformis", "strain": "strain=CAM-8", "accession": "GCA_014243445.1", "taxid": 2045119, "species_taxid": 2045119, "relation_to_type": "type", "validated": true, "ani": 82.3083, "matched_fragments": 836, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquarius", "strain": "strain=HYN0069", "accession": "GCA_003060865.1", "taxid": 2169400, "species_taxid": 2169400, "relation_to_type": "type", "validated": true, "ani": 81.3939, "matched_fragments": 792, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhodobacter flagellatus", "strain": "strain=SYSU G03088", "accession": "GCA_008271465.1", "taxid": 2593021, "species_taxid": 2593021, "relation_to_type": "type", "validated": true, "ani": 80.4151, "matched_fragments": 675, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter aquatilis", "strain": "strain=DSM 3857", "accession": "GCA_900110025.1", "taxid": 933059, "species_taxid": 933059, "relation_to_type": "type", "validated": true, "ani": 80.1623, "matched_fragments": 661, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter lutimaris", "strain": "strain=YJ-T1-11", "accession": "GCA_003570715.1", "taxid": 2306023, "species_taxid": 2306023, "relation_to_type": "type", "validated": true, "ani": 79.8698, "matched_fragments": 643, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemmobacter fulva", "strain": "strain=con5", "accession": "GCA_018798885.1", "taxid": 2840474, "species_taxid": 2840474, "relation_to_type": "type", "validated": true, "ani": 79.7708, "matched_fragments": 626, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter ovatus", "strain": "strain=JA234", "accession": "GCA_900207575.1", "taxid": 439529, "species_taxid": 439529, "relation_to_type": "type", "validated": true, "ani": 79.5173, "matched_fragments": 558, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cereibacter sediminicola", "strain": "strain=JA983", "accession": "GCA_007668225.1", "taxid": 2584941, "species_taxid": 2584941, "relation_to_type": "type", "validated": true, "ani": 79.4389, "matched_fragments": 552, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseicitreum antarcticum", "strain": "strain=ZS2-28", "accession": "GCA_014681765.1", "taxid": 564137, "species_taxid": 564137, "relation_to_type": "type", "validated": true, "ani": 77.5605, "matched_fragments": 342, "total_fragments": 1363, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_009908265.2", "gtdb_species": "s__Gemmobacter_B sp009908265", "ani": 100.0, "matched_fragments": 1362, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B", "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": "GCA_000500915.1", "gtdb_species": "s__Gemmobacter_B sp000500915", "ani": 86.7096, "matched_fragments": 828, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_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_011059185.1", "gtdb_species": "s__Gemmobacter_B sp011059185", "ani": 85.6988, "matched_fragments": 947, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_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_002855575.1", "gtdb_species": "s__Gemmobacter_B sp002855575", "ani": 85.3816, "matched_fragments": 961, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_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_014654775.1", "gtdb_species": "s__Gemmobacter_B sp014654775", "ani": 84.6338, "matched_fragments": 914, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_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_009908315.1", "gtdb_species": "s__Gemmobacter_B sp009908315", "ani": 84.5703, "matched_fragments": 873, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_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_014859945.1", "gtdb_species": "s__UBA1943 sp014859945", "ani": 80.4749, "matched_fragments": 516, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943", "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_002256185.1", "gtdb_species": "s__Gemmobacter_B sp002256185", "ani": 80.1681, "matched_fragments": 671, "total_fragments": 1363, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_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": -0.102, "cell_length": 0.166, "doubling_h": 0.531, "growth_tmp": 28.333, "optimum_tmp": 30.312, "optimum_ph": 6.9, "genome_size": 4127409.974, "gc_content": 66.914, "coding_genes": 3782.589, "rRNA16S_genes": 3.9, "tRNA_genes": 50.925, "gram_stain": 0.0, "sporulation": 0.2, "motility": 0.625, "range_salinity": 0.0, "facultative_respiration": 0.333, "anaerobic_respiration": 0.333, "aerobic_respiration": 0.333, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.5, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.5, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Rhodobacter", "amnigenus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }