{ "type": "genome", "identifier": "GCF_026162625.1", "organism": "Paracoccus beibuensis", "title": "Paracoccus beibuensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Third Institute of Oceanography, Ministry of Natural Resources", "publication": [ {} ], "properties": { "assembly_accession": "GCF_026162625.1", "bioproject": "PRJNA224116", "biosample": "SAMN31098258", "wgs_master": "JAOTBD000000000.1", "refseq_category": "reference genome", "taxid": "547602", "species_taxid": "547602", "organism_name": "Paracoccus beibuensis", "infraspecific_name": "strain=CGMCC 1.7295", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/11/13", "asm_name": "ASM2616262v1", "asm_submitter": "Third Institute of Oceanography, Ministry of Natural Resources", "gbrs_paired_asm": "GCA_026162625.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/026/162/625/GCF_026162625.1_ASM2616262v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3942873", "genome_size_ungapped": "3942873", "gc_percent": "66.000000", "replicon_count": "0", "scaffold_count": "99", "contig_count": "99", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_026162625.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4015", "protein_coding_gene_count": "3799", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-11-13", "dateModified": "2022-11-13", "datePublished": "2022-11-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Paracoccus beibuensis" ], "sample_taxid": [ "547602" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.090 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)": "3942873", "Number of Sequences": "99", "Longest Sequences (bp)": "314776", "N50 (bp)": "93228", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.0", "Number of CDSs": "3896", "Average Protein Length": "296.8", "Coding Ratio (%)": "88.0", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paracoccus liaowanqingii", "strain": "strain=2251", "accession": "GCA_004683865.2", "taxid": 2560053, "species_taxid": 2560053, "relation_to_type": "type", "validated": true, "ani": 84.1247, "matched_fragments": 837, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus hibiscisoli", "strain": "strain=CCTCC AB2016182", "accession": "GCA_005048265.1", "taxid": 2023261, "species_taxid": 2023261, "relation_to_type": "type", "validated": true, "ani": 83.9682, "matched_fragments": 778, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus gahaiensis", "strain": "strain=KCTC 42687", "accession": "GCA_005048225.1", "taxid": 1706839, "species_taxid": 1706839, "relation_to_type": "type", "validated": true, "ani": 83.8642, "matched_fragments": 815, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aestuarii", "strain": "strain=DSM 19484", "accession": "GCA_003594815.1", "taxid": 453842, "species_taxid": 453842, "relation_to_type": "type", "validated": true, "ani": 83.8502, "matched_fragments": 711, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus zeaxanthinifaciens", "strain": "strain=ATCC 21588", "accession": "GCA_000420145.1", "taxid": 187400, "species_taxid": 187400, "relation_to_type": "type", "validated": true, "ani": 83.2501, "matched_fragments": 660, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus indicus", "strain": "strain=IO390502", "accession": "GCA_003056335.1", "taxid": 2079229, "species_taxid": 2079229, "relation_to_type": "type", "validated": true, "ani": 83.0011, "matched_fragments": 748, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus tibetensis", "strain": "strain=CGMCC 1.8925", "accession": "GCA_900102505.1", "taxid": 336292, "species_taxid": 336292, "relation_to_type": "type", "validated": true, "ani": 82.816, "matched_fragments": 754, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus nototheniae", "strain": "strain=I-41R45", "accession": "GCA_004335005.1", "taxid": 2489002, "species_taxid": 2489002, "relation_to_type": "type", "validated": true, "ani": 82.6331, "matched_fragments": 753, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus fontiphilus", "strain": "strain=MVW-1", "accession": "GCA_017356265.1", "taxid": 1815556, "species_taxid": 1815556, "relation_to_type": "type", "validated": true, "ani": 82.5599, "matched_fragments": 673, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus shandongensis", "strain": "strain=wg2", "accession": "GCA_017315735.1", "taxid": 2816048, "species_taxid": 2816048, "relation_to_type": "type", "validated": true, "ani": 82.4315, "matched_fragments": 680, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aerius", "strain": "strain=KCTC 42845", "accession": "GCA_016757275.1", "taxid": 1915382, "species_taxid": 1915382, "relation_to_type": "type", "validated": true, "ani": 81.9876, "matched_fragments": 690, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aerius", "strain": "strain=KCTC 42845", "accession": "GCA_014656455.1", "taxid": 1915382, "species_taxid": 1915382, "relation_to_type": "type", "validated": true, "ani": 81.9505, "matched_fragments": 700, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus everestensis", "strain": "strain=S8-55", "accession": "GCA_021491915.1", "taxid": 2903900, "species_taxid": 2903900, "relation_to_type": "type", "validated": true, "ani": 81.2537, "matched_fragments": 610, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus salsus", "strain": "strain=EGI L200073", "accession": "GCA_021556615.1", "taxid": 2911061, "species_taxid": 2911061, "relation_to_type": "type", "validated": true, "ani": 80.7583, "matched_fragments": 598, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus tegillarcae", "strain": "strain=BM15", "accession": "GCA_002847305.1", "taxid": 1529068, "species_taxid": 1529068, "relation_to_type": "type", "validated": true, "ani": 79.3835, "matched_fragments": 478, "total_fragments": 1260, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_006151785.1", "gtdb_species": "s__Paracoccus marcusii", "ani": 84.1485, "matched_fragments": 716, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.50", "min_intra_species_ani": "96.78", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.75", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_004683865.2", "gtdb_species": "s__Paracoccus liaowanqingii", "ani": 84.0961, "matched_fragments": 839, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.54", "min_intra_species_ani": "96.54", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005048265.1", "gtdb_species": "s__Paracoccus hibiscisoli", "ani": 83.9803, "matched_fragments": 777, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.40", "min_intra_species_ani": "96.40", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005048225.1", "gtdb_species": "s__Paracoccus gahaiensis", "ani": 83.8866, "matched_fragments": 813, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_003594815.1", "gtdb_species": "s__Paracoccus aestuarii", "ani": 83.8295, "matched_fragments": 712, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_000787695.1", "gtdb_species": "s__Paracoccus sp000787695", "ani": 83.6964, "matched_fragments": 720, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_003255745.1", "gtdb_species": "s__Paracoccus saliphilus_A", "ani": 83.6569, "matched_fragments": 759, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_016869875.1", "gtdb_species": "s__Paracoccus sp016869875", "ani": 83.3458, "matched_fragments": 591, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_003056335.1", "gtdb_species": "s__Paracoccus indicus", "ani": 83.0011, "matched_fragments": 748, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_900102505.1", "gtdb_species": "s__Paracoccus tibetensis", "ani": 82.8273, "matched_fragments": 753, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_017356265.1", "gtdb_species": "s__Paracoccus fontiphilus", "ani": 82.5837, "matched_fragments": 671, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "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_014656455.1", "gtdb_species": "s__Paracoccus aerius", "ani": 81.9371, "matched_fragments": 701, "total_fragments": 1260, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.84", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.225, "cell_length": 0.052, "doubling_h": 0.322, "growth_tmp": 29.985, "optimum_tmp": 28.863, "optimum_ph": 7.854, "genome_size": 3978575.325, "gc_content": 67.295, "coding_genes": 3755.444, "rRNA16S_genes": 3.0, "tRNA_genes": 52.0, "gram_stain": 0.029, "sporulation": 0.0, "motility": 0.117, "range_salinity": null, "facultative_respiration": 0.062, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.937, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.647, "coccus_cell_shape": 0.294, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.058, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Paracoccus", "beibuensis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }