{ "type": "genome", "identifier": "GCF_009833085.1", "organism": "Nitrosomonas oligotropha", "title": "Nitrosomonas oligotropha", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Miami University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009833085.1", "bioproject": "PRJNA224116", "biosample": "SAMN03704077", "wgs_master": "QRBZ00000000.1", "refseq_category": "reference genome", "taxid": "42354", "species_taxid": "42354", "organism_name": "Nitrosomonas oligotropha", "infraspecific_name": "strain=Nm45", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/01/07", "asm_name": "ASM983308v1", "asm_submitter": "Miami University", "gbrs_paired_asm": "GCA_009833085.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/833/085/GCF_009833085.1_ASM983308v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3119926", "genome_size_ungapped": "3119926", "gc_percent": "49.000000", "replicon_count": "0", "scaffold_count": "70", "contig_count": "70", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009833085.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2947", "protein_coding_gene_count": "2863", "non_coding_gene_count": "45", "pubmed_id": "30976841" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-01-07", "dateModified": "2020-01-07", "datePublished": "2020-01-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Nitrosomonas oligotropha" ], "sample_taxid": [ "42354" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Germany: Hamburg" ], "sample_host_location_id": [], "data_size": "0.892 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3119926", "Number of Sequences": "70", "Longest Sequences (bp)": "184737", "N50 (bp)": "90587", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "49.2", "Number of CDSs": "2838", "Average Protein Length": "317.7", "Coding Ratio (%)": "86.7", "Number of rRNAs": "3", "Number of tRNAs": "38", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Nitrosomonas oligotropha", "strain": "strain=Nm45", "accession": "GCA_009833085.1", "taxid": 42354, "species_taxid": 42354, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1006, "total_fragments": 1010, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Nitrosomonas ureae", "strain": "strain=Nm10", "accession": "GCA_900105875.1", "taxid": 44577, "species_taxid": 44577, "relation_to_type": "type", "validated": true, "ani": 78.1452, "matched_fragments": 277, "total_fragments": 1010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrosomonas ureae", "strain": "strain=Nm10", "accession": "GCA_001455205.1", "taxid": 44577, "species_taxid": 44577, "relation_to_type": "type", "validated": true, "ani": 78.0799, "matched_fragments": 278, "total_fragments": 1010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrosomonas supralitoralis", "strain": "strain=APG5", "accession": "GCA_003011925.2", "taxid": 2116706, "species_taxid": 2116706, "relation_to_type": "type", "validated": true, "ani": 77.6355, "matched_fragments": 252, "total_fragments": 1010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrosospira lacus", "strain": "strain=APG3", "accession": "GCA_000355765.4", "taxid": 1288494, "species_taxid": 1288494, "relation_to_type": "type", "validated": true, "ani": 76.6876, "matched_fragments": 67, "total_fragments": 1010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrosomonas europaea", "strain": "strain=ATCC 25978", "accession": "GCA_900167395.1", "taxid": 915, "species_taxid": 915, "relation_to_type": "type", "validated": true, "ani": 76.6575, "matched_fragments": 57, "total_fragments": 1010, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrosospira briensis", "strain": "strain=C-128", "accession": "GCA_000619905.2", "taxid": 35799, "species_taxid": 35799, "relation_to_type": "reftype", "validated": true, "ani": 76.2108, "matched_fragments": 57, "total_fragments": 1010, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { 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"s__Nitrosomonas sp018240285", "ani": 81.7928, "matched_fragments": 656, "total_fragments": 1010, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.27", "min_intra_species_ani": "97.27", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.097, "cell_length": 0.041, "doubling_h": 0.74, "growth_tmp": 27.75, "optimum_tmp": 27.2, "optimum_ph": 7.5, "genome_size": 3354976.667, "gc_content": 46.767, "coding_genes": 2822.875, "rRNA16S_genes": 1.0, "tRNA_genes": 40.75, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.666, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, 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