{ "type": "genome", "identifier": "GCF_002287065.1", "organism": "Paracoccus salipaludis", "title": "Paracoccus salipaludis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002287065.1", "bioproject": "PRJNA224116", "biosample": "SAMN07572621", "wgs_master": "NSJZ00000000.1", "refseq_category": "reference genome", "taxid": "2032623", "species_taxid": "2032623", "organism_name": "Paracoccus salipaludis", "infraspecific_name": "strain=WN007", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/09/06", "asm_name": "ASM228706v1", "asm_submitter": "Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences", "gbrs_paired_asm": "GCA_002287065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/287/065/GCF_002287065.1_ASM228706v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3674522", "genome_size_ungapped": "3674522", "gc_percent": "68.500000", "replicon_count": "0", "scaffold_count": "187", "contig_count": "187", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002287065.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "3701", "protein_coding_gene_count": "3543", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-09-06", "dateModified": "2017-09-06", "datePublished": "2017-09-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Paracoccus salipaludis" ], "sample_taxid": [ "2032623" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Binhai, Tianjin" ], "sample_host_location_id": [], "data_size": "0.999 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 33.0, "max": 33.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3674522", "Number of Sequences": "187", "Longest Sequences (bp)": "549325", "N50 (bp)": "250697", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "68.6", "Number of CDSs": "3454", "Average Protein Length": "311.1", "Coding Ratio (%)": "87.7", "Number of rRNAs": "4", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paracoccus salipaludis", "strain": "strain=WN007", "accession": "GCA_002287065.1", "taxid": 2032623, "species_taxid": 2032623, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1159, "total_fragments": 1163, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paracoccus chinensis", "strain": "strain=CGMCC 1.7655", "accession": "GCA_900102885.1", "taxid": 525640, "species_taxid": 525640, "relation_to_type": "type", "validated": true, "ani": 90.9163, "matched_fragments": 923, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus sphaerophysae", "strain": "strain=HAMBI 3106", "accession": "GCA_000763805.1", "taxid": 690417, "species_taxid": 690417, "relation_to_type": "type", "validated": true, "ani": 83.6507, "matched_fragments": 699, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus solventivorans", "strain": "strain=DSM 6637", "accession": "GCA_900142875.1", "taxid": 53463, "species_taxid": 53463, "relation_to_type": "type", "validated": true, "ani": 83.639, "matched_fragments": 691, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus sanguinis", "strain": "strain=DSM 29303", "accession": "GCA_900106665.1", "taxid": 1545044, "species_taxid": 1545044, "relation_to_type": "type", "validated": true, "ani": 83.3886, "matched_fragments": 736, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus endophyticus", "strain": "strain=SYSUP0003", "accession": "GCA_003286075.1", "taxid": 2233774, "species_taxid": 2233774, "relation_to_type": "type", "validated": true, "ani": 83.3283, "matched_fragments": 698, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus luteus", "strain": "strain=CFH 10530", "accession": "GCA_004522155.1", "taxid": 2508543, "species_taxid": 2508543, "relation_to_type": "type", "validated": true, "ani": 83.3013, "matched_fragments": 703, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus alkenifer", "strain": "strain=DSM 11593", "accession": "GCA_900108405.1", "taxid": 65735, "species_taxid": 65735, "relation_to_type": "type", "validated": true, "ani": 82.6025, "matched_fragments": 648, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus aeridis", "strain": "strain=JC501", "accession": "GCA_004923205.2", "taxid": 1966466, "species_taxid": 1966466, "relation_to_type": "type", "validated": true, "ani": 82.439, "matched_fragments": 652, "total_fragments": 1163, "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": 81.5847, "matched_fragments": 619, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus mutanolyticus", "strain": "strain=RSP-02", "accession": "GCA_003285265.1", "taxid": 1499308, "species_taxid": 1499308, "relation_to_type": "type", "validated": true, "ani": 81.0308, "matched_fragments": 588, "total_fragments": 1163, "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": 79.956, "matched_fragments": 508, "total_fragments": 1163, "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": 79.0877, "matched_fragments": 458, "total_fragments": 1163, "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": 78.2957, "matched_fragments": 383, "total_fragments": 1163, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002287065.1", "gtdb_species": "s__Paracoccus salipaludis", "ani": 100.0, "matched_fragments": 1159, "total_fragments": 1163, "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": "conclusive" }, { "accession": "GCF_900102885.1", "gtdb_species": "s__Paracoccus chinensis", "ani": 90.8984, "matched_fragments": 924, "total_fragments": 1163, "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_016617715.1", "gtdb_species": "s__Paracoccus sp014164625", "ani": 87.0729, "matched_fragments": 827, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.50", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900142875.1", "gtdb_species": "s__Paracoccus solventivorans", "ani": 83.6655, "matched_fragments": 689, "total_fragments": 1163, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.61", "min_intra_species_ani": "95.99", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000763805.1", "gtdb_species": "s__Paracoccus sphaerophysae", "ani": 83.6089, "matched_fragments": 703, "total_fragments": 1163, "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_003286075.1", "gtdb_species": "s__Paracoccus endophyticus", "ani": 83.3155, "matched_fragments": 699, "total_fragments": 1163, "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_004522155.1", "gtdb_species": "s__Paracoccus luteus", "ani": 83.2677, "matched_fragments": 706, "total_fragments": 1163, "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_900108405.1", "gtdb_species": "s__Paracoccus alkenifer", "ani": 82.6229, "matched_fragments": 646, "total_fragments": 1163, "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_004923205.2", "gtdb_species": "s__Paracoccus aeridis", "ani": 82.4721, "matched_fragments": 650, "total_fragments": 1163, "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": "-" } ] }, "_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", "salipaludis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }