{ "type": "genome", "identifier": "GCA_013373445.1", "organism": "Paracoccaceae bacterium", "title": "Paracoccaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "University of Georgia", "publication": [ {} ], "properties": { "assembly_accession": "GCA_013373445.1", "bioproject": "PRJNA553557", "biosample": "SAMN14488405", "wgs_master": "JABXHV000000000.1", "refseq_category": "na", "taxid": "1904441", "species_taxid": "1904441", "organism_name": "Paracoccaceae bacterium", "infraspecific_name": "", "isolate": "HF-Dia03", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/25", "asm_name": "ASM1337344v1", "submitter": "University of Georgia", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/373/445/GCA_013373445.1_ASM1337344v1", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-25", "dateModified": "2020-06-25", "datePublished": "2020-06-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Paracoccaceae bacterium" ], "sample_taxid": [ "1904441" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Georgia, Sapelo Island" ], "sample_host_location_id": [], "data_size": "1.045 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 96.3, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3641490", "Number of Sequences": "201", "Longest Sequences (bp)": "120567", "N50 (bp)": "31207", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.1", "Number of CDSs": "3216", "Average Protein Length": "309.4", "Coding Ratio (%)": "82.0", "Number of rRNAs": "0", "Number of tRNAs": "32", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Roseibium limicola", "strain": "strain=CAU 1637", "accession": "GCA_017313085.1", "taxid": 2816037, "species_taxid": 2816037, "relation_to_type": "type", "validated": true, "ani": 77.1996, "matched_fragments": 193, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium polysiphoniae", "strain": "strain=KACC 19711", "accession": "GCA_014842925.1", "taxid": 2571221, "species_taxid": 2571221, "relation_to_type": "type", "validated": true, "ani": 77.1853, "matched_fragments": 216, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium alexandrii", "strain": "strain=DFL-11", "accession": "GCA_000158095.2", "taxid": 388408, "species_taxid": 388408, "relation_to_type": "type", "validated": true, "ani": 77.1805, "matched_fragments": 135, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium marinum", "strain": "strain=DSM 17023", "accession": "GCA_002906165.1", "taxid": 281252, "species_taxid": 281252, "relation_to_type": "type", "validated": true, "ani": 76.995, "matched_fragments": 149, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium suaedae", "strain": "strain=DSM 22153", "accession": "GCA_900142725.1", "taxid": 735517, "species_taxid": 735517, "relation_to_type": "type", "validated": true, "ani": 76.976, "matched_fragments": 212, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium litorale", "strain": "strain=4C16A", "accession": "GCA_014842915.1", "taxid": 2803841, "species_taxid": 2803841, "relation_to_type": "type", "validated": true, "ani": 76.913, "matched_fragments": 187, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium aggregatum", "strain": "strain=IAM 12614", "accession": "GCA_000168975.1", "taxid": 187304, "species_taxid": 187304, "relation_to_type": "suspected-type", "validated": true, "ani": 76.8464, "matched_fragments": 156, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Roseibium sediminis", "strain": "strain=KCTC 52373", "accession": "GCA_008711325.1", "taxid": 1775174, "species_taxid": 1775174, "relation_to_type": "type", "validated": true, "ani": 76.7884, "matched_fragments": 160, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter carbonis", "strain": "strain=Q4.6", "accession": "GCA_003012935.1", "taxid": 2067569, "species_taxid": 2067569, "relation_to_type": "type", "validated": true, "ani": 76.2042, "matched_fragments": 130, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stappia albiluteola", "strain": "strain=F7233", "accession": "GCA_014050225.1", "taxid": 2758565, "species_taxid": 2758565, "relation_to_type": "type", "validated": true, "ani": 76.0753, "matched_fragments": 68, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rhizobium daejeonense", "strain": "strain=L61", "accession": "GCA_014280875.1", "taxid": 240521, "species_taxid": 240521, "relation_to_type": "type", "validated": true, "ani": 75.5932, "matched_fragments": 55, "total_fragments": 1120, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 96.3, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_013373445.1", "gtdb_species": "s__Roseibium sp013373445", "ani": 100.0, "matched_fragments": 1108, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_017313085.1", "gtdb_species": "s__Roseibium sp017313085", "ani": 77.1849, "matched_fragments": 194, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_014842925.1", "gtdb_species": "s__Roseibium polysiphoniae", "ani": 77.1732, "matched_fragments": 217, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.20", "min_intra_species_ani": "96.20", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007830545.1", "gtdb_species": "s__Roseibium hamelinense", "ani": 77.1102, "matched_fragments": 109, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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": "GCF_002237595.1", "gtdb_species": "s__Roseibium sp002237595", "ani": 77.0828, "matched_fragments": 173, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_009650605.1", "gtdb_species": "s__Roseibium sp009650605", "ani": 77.0114, "matched_fragments": 205, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_002906165.1", "gtdb_species": "s__Roseibium marinum", "ani": 76.995, "matched_fragments": 149, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_001890945.1", "gtdb_species": "s__Roseibium sp001890945", "ani": 76.8617, "matched_fragments": 134, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.65", "min_intra_species_ani": "95.54", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000148725.1", "gtdb_species": "s__Roseibium sp000148725", "ani": 76.8567, "matched_fragments": 129, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_006517275.1", "gtdb_species": "s__Roseibium sp006517275", "ani": 76.8564, "matched_fragments": 137, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_003075075.1", "gtdb_species": "s__Roseibium sp003075075", "ani": 76.8281, "matched_fragments": 159, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_014692675.1", "gtdb_species": "s__Roseibium aggregatum_C", "ani": 76.8202, "matched_fragments": 193, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_001999245.1", "gtdb_species": "s__Roseibium aggregatum_A", "ani": 76.7924, "matched_fragments": 169, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.61", "min_intra_species_ani": "96.85", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.89", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_008711325.1", "gtdb_species": "s__Roseibium sediminis", "ani": 76.7884, "matched_fragments": 160, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_001404055.1", "gtdb_species": "s__Roseibium album_A", "ani": 76.578, "matched_fragments": 123, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium", "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_000192745.1", "gtdb_species": "s__Polymorphum gilvum", "ani": 76.3387, "matched_fragments": 112, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum", "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_009826895.1", "gtdb_species": "s__Hongsoonwoonella sp009826895", "ani": 76.3009, "matched_fragments": 75, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella", "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_003012935.1", "gtdb_species": "s__Pannonibacter carbonis", "ani": 76.2042, "matched_fragments": 130, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter", "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_002709505.1", "gtdb_species": "s__Stappia sp002709505", "ani": 75.6062, "matched_fragments": 69, "total_fragments": 1120, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Stappiaceae", "g__Roseibium", "s__Roseibium sp013373445" ], "_genome_taxon": [ "Paracoccaceae", "bacterium", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Rhizobiales", "f__Stappiaceae", "g__Roseibium", "s__Roseibium sp013373445", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Rhizobiales", "Stappiaceae", "Roseibium", "Roseibium", "sp013373445" ], "_meo": [ { "id": "MEO_0000041", "label": "marine water" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }