{ "type": "genome", "identifier": "GCF_008727795.1", "organism": "Nitrincola iocasae", "title": "Nitrincola iocasae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Oceanology, Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008727795.1", "bioproject": "PRJNA224116", "biosample": "SAMN12792670", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2614693", "species_taxid": "2614693", "organism_name": "Nitrincola iocasae", "infraspecific_name": "strain=KXZD1103", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/29", "asm_name": "ASM872779v1", "asm_submitter": "Institute of Oceanology, Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_008727795.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/727/795/GCF_008727795.1_ASM872779v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4172991", "genome_size_ungapped": "4172991", "gc_percent": "50.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008727795.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3889", "protein_coding_gene_count": "3788", "non_coding_gene_count": "77", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-29", "dateModified": "2019-09-29", "datePublished": "2019-09-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Nitrincola iocasae" ], "sample_taxid": [ "2614693" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.187 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)": "4172991", "Number of Sequences": "2", "Longest Sequences (bp)": "4129232", "N50 (bp)": "4129232", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "50.1", "Number of CDSs": "3841", "Average Protein Length": "329.5", "Coding Ratio (%)": "91.0", "Number of rRNAs": "15", "Number of tRNAs": "56", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nitrincola iocasae", "strain": "strain=KXZD1103", "accession": "GCA_008727795.1", "taxid": 2614693, "species_taxid": 2614693, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1390, "total_fragments": 1390, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nitrincola lacisaponensis", "strain": "strain=4CA", "accession": "GCA_000691225.1", "taxid": 267850, "species_taxid": 267850, "relation_to_type": "type", "validated": true, "ani": 78.8525, "matched_fragments": 487, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphritea ceti", "strain": "strain=KCTC 42154", "accession": "GCA_024347215.1", "taxid": 1524258, "species_taxid": 1524258, "relation_to_type": "type", "validated": true, "ani": 78.751, "matched_fragments": 71, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrincola schmidtii", "strain": "strain=NCAIM B.02626", "accession": "GCA_008973715.1", "taxid": 1730894, "species_taxid": 1730894, "relation_to_type": "type", "validated": true, "ani": 78.4468, "matched_fragments": 246, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium aestuarii", "strain": "strain=ST58-10", "accession": "GCA_001651805.1", "taxid": 1821621, "species_taxid": 1821621, "relation_to_type": "type", "validated": true, "ani": 78.1982, "matched_fragments": 102, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphritea japonica", "strain": "strain=ATCC BAA-1530", "accession": "GCA_016592435.1", "taxid": 452627, "species_taxid": 452627, "relation_to_type": "type", "validated": true, "ani": 78.1003, "matched_fragments": 78, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrincola alkalilacustris", "strain": "strain=NCAIM B.02612", "accession": "GCA_008973755.1", "taxid": 1571224, "species_taxid": 1571224, "relation_to_type": "type", "validated": true, "ani": 77.7694, "matched_fragments": 199, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium halophilum", "strain": "strain=DSM 17586", "accession": "GCA_003014615.1", "taxid": 267374, "species_taxid": 267374, "relation_to_type": "type", "validated": true, "ani": 77.66, "matched_fragments": 124, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrincola tapanii", "strain": "strain=MEB193", "accession": "GCA_008368715.1", "taxid": 1708751, "species_taxid": 1708751, "relation_to_type": "type", "validated": true, "ani": 77.6585, "matched_fragments": 181, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium mangrovicola", "strain": "strain=DSM 27697", "accession": "GCA_004339595.1", "taxid": 1476959, "species_taxid": 1476959, "relation_to_type": "type", "validated": true, "ani": 77.4852, "matched_fragments": 107, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium georgiense", "strain": "strain=DSM 11526", "accession": "GCA_900107855.1", "taxid": 48076, "species_taxid": 48076, "relation_to_type": "type", "validated": true, "ani": 77.473, "matched_fragments": 129, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium ramblicola", "strain": "strain=D7", "accession": "GCA_019084545.1", "taxid": 2849041, "species_taxid": 2849041, "relation_to_type": "type", "validated": true, "ani": 77.0714, "matched_fragments": 101, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphritea spongicola", "strain": "strain=JCM 16668", "accession": "GCA_017051665.1", "taxid": 707589, "species_taxid": 707589, "relation_to_type": "type", "validated": true, "ani": 76.9596, "matched_fragments": 86, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphritea atlantica", "strain": "strain=DSM 18887", "accession": "GCA_900111095.1", "taxid": 355243, "species_taxid": 355243, "relation_to_type": "type", "validated": true, "ani": 76.373, "matched_fragments": 93, "total_fragments": 1390, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_008727795.1", "gtdb_species": "s__Nitrincola sp008727795", "ani": 100.0, "matched_fragments": 1390, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola", "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_000764495.1", "gtdb_species": "s__Nitrincola sp000764495", "ani": 84.4923, "matched_fragments": 876, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola", "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_000691225.1", "gtdb_species": "s__Nitrincola lacisaponensis", "ani": 78.8426, "matched_fragments": 488, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola", "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_008973715.1", "gtdb_species": "s__Nitrincola schmidtii", "ani": 78.4468, "matched_fragments": 246, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola", "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_007693685.1", "gtdb_species": "s__Nitrincola sp007693685", "ani": 78.209, "matched_fragments": 196, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola", "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_008973755.1", "gtdb_species": "s__Nitrincola alkalilacustris", "ani": 77.7915, "matched_fragments": 199, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola", "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_008368715.1", "gtdb_species": "s__Nitrincola tapanii", "ani": 77.6585, "matched_fragments": 181, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola", "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_004339595.1", "gtdb_species": "s__Marinobacterium mangrovicola", "ani": 77.4852, "matched_fragments": 107, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_900107855.1", "gtdb_species": "s__Marinobacterium georgiense", "ani": 77.4461, "matched_fragments": 128, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.23", "min_intra_species_ani": "97.23", "mean_intra_species_af": "0.75", "min_intra_species_af": "0.75", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_019061305.1", "gtdb_species": "s__Marinobacterium sp019061305", "ani": 77.2048, "matched_fragments": 111, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_019084545.1", "gtdb_species": "s__Marinobacterium sp019084545", "ani": 77.0932, "matched_fragments": 99, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_003250495.1", "gtdb_species": "s__Marinobacterium sp003250495", "ani": 77.0464, "matched_fragments": 79, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium", "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_017051665.1", "gtdb_species": "s__Amphritea spongicola", "ani": 76.9595, "matched_fragments": 87, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea", "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_900111095.1", "gtdb_species": "s__Amphritea atlantica", "ani": 76.3929, "matched_fragments": 92, "total_fragments": 1390, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea", "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": -0.302, "cell_length": 0.146, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 9.0, "genome_size": 3412133.0, "gc_content": 52.069, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Nitrincola", "iocasae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }