{ "type": "genome", "identifier": "GCF_004335005.1", "organism": "Paracoccus nototheniae", "title": "Paracoccus nototheniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Universidad Andres Bello", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004335005.1", "bioproject": "PRJNA224116", "biosample": "SAMN10432241", "wgs_master": "RQRT00000000.1", "refseq_category": "reference genome", "taxid": "2489002", "species_taxid": "2489002", "organism_name": "Paracoccus nototheniae", "infraspecific_name": "strain=I-41R45", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/08", "asm_name": "ASM433500v1", "asm_submitter": "Universidad Andres Bello", "gbrs_paired_asm": "GCA_004335005.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/335/005/GCF_004335005.1_ASM433500v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4597015", "genome_size_ungapped": "4597015", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "235", "contig_count": "235", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004335005.1-RS_2024_04_11", "annotation_date": "2024-04-11", "total_gene_count": "4560", "protein_coding_gene_count": "4421", "non_coding_gene_count": "49", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-08", "dateModified": "2019-03-08", "datePublished": "2019-03-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Paracoccus nototheniae" ], "sample_taxid": [ "2489002" ], "sample_host_organism": [ "Notothenia coriiceps (black rock cod)" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica: Chile" ], "sample_host_location_id": [], "data_size": "1.269 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)": "4597015", "Number of Sequences": "235", "Longest Sequences (bp)": "211322", "N50 (bp)": "51739", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.3", "Number of CDSs": "4373", "Average Protein Length": "306.2", "Coding Ratio (%)": "87.4", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paracoccus nototheniae", "strain": "strain=I-41R45", "accession": "GCA_004335005.1", "taxid": 2489002, "species_taxid": 2489002, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1425, "total_fragments": 1440, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Paracoccus gahaiensis", "strain": "strain=KCTC 42687", "accession": "GCA_005048225.1", "taxid": 1706839, "species_taxid": 1706839, "relation_to_type": "type", "validated": true, "ani": 87.088, "matched_fragments": 969, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus liaowanqingii", "strain": "strain=2251", "accession": "GCA_004683865.2", "taxid": 2560053, "species_taxid": 2560053, "relation_to_type": "type", "validated": true, "ani": 86.8563, "matched_fragments": 973, "total_fragments": 1440, "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": 85.5958, "matched_fragments": 881, "total_fragments": 1440, "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": 84.5571, "matched_fragments": 748, "total_fragments": 1440, "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": 82.7904, "matched_fragments": 763, "total_fragments": 1440, "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": 81.5039, "matched_fragments": 698, "total_fragments": 1440, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paracoccus 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"s__Paracoccus sp016869875", "ani": 82.2273, "matched_fragments": 577, "total_fragments": 1440, "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", "nototheniae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }