{ "type": "genome", "identifier": "GCA_024282095.1", "organism": "Nitrosomonas sp.", "title": "Nitrosomonas sp.", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "Northeastern University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_024282095.1", "bioproject": "PRJNA846349", "biosample": "SAMN28968170", "wgs_master": "JAMWZS000000000.1", "refseq_category": "na", "taxid": "42353", "species_taxid": "42353", "organism_name": "Nitrosomonas sp.", "infraspecific_name": "", "isolate": "GRE_AOB_3", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/07/15", "asm_name": "ASM2428209v1", "submitter": "Northeastern University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/024/282/095/GCA_024282095.1_ASM2428209v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-07-15", "dateModified": "2022-07-15", "datePublished": "2022-07-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Nitrosomonas sp." ], "sample_taxid": [ "42353" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Pennsylvania" ], "sample_host_location_id": [], "data_size": "0.802 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2799191", "Number of Sequences": "81", "Longest Sequences (bp)": "186128", "N50 (bp)": "54702", "Gap Ratio (%)": "0.000036", "GCcontent (%)": "46.4", "Number of CDSs": "2469", "Average Protein Length": "322.1", "Coding Ratio (%)": "85.2", "Number of rRNAs": "0", "Number of tRNAs": "28", "Number of CRISPRs": "0" }, "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": 78.2779, "matched_fragments": 357, "total_fragments": 896, "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": 78.0273, "matched_fragments": 291, "total_fragments": 896, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrosomonas ureae", "strain": "strain=Nm10", "accession": "GCA_900105875.1", "taxid": 44577, "species_taxid": 44577, "relation_to_type": "type", "validated": true, "ani": 77.9994, "matched_fragments": 291, "total_fragments": 896, "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": 77.5157, "matched_fragments": 290, "total_fragments": 896, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003201565.1", "gtdb_species": "s__Nitrosomonas sp003201565", "ani": 90.5928, "matched_fragments": 734, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_017984435.1", "gtdb_species": "s__Nitrosomonas sp017984435", "ani": 82.063, "matched_fragments": 546, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000219585.1", "gtdb_species": "s__Nitrosomonas sp000219585", "ani": 79.8639, "matched_fragments": 505, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "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_016708955.1", "gtdb_species": "s__Nitrosomonas sp016708955", "ani": 79.7984, "matched_fragments": 431, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "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_016721865.1", "gtdb_species": "s__Nitrosomonas sp016721865", "ani": 79.6956, "matched_fragments": 448, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "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_900112825.1", "gtdb_species": "s__Nitrosomonas sp900112825", "ani": 79.2388, "matched_fragments": 455, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "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_017994575.1", "gtdb_species": "s__Nitrosomonas sp017994575", "ani": 78.7924, "matched_fragments": 321, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.80", "min_intra_species_ani": "99.80", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902826115.1", "gtdb_species": "s__Nitrosomonas sp902826115", "ani": 78.6911, "matched_fragments": 374, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.11", "min_intra_species_ani": "98.94", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900106555.1", "gtdb_species": "s__Nitrosomonas oligotropha_A", "ani": 78.4293, "matched_fragments": 344, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.13", "min_intra_species_ani": "95.07", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.80", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_002083595.1", "gtdb_species": "s__Nitrosomonas sp002083595", "ani": 78.2845, "matched_fragments": 309, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "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_004345375.1", "gtdb_species": "s__Nitrosomonas sp004345375", "ani": 78.2581, "matched_fragments": 346, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "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_015709635.1", "gtdb_species": "s__Nitrosomonas sp015709635", "ani": 78.2206, "matched_fragments": 323, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.39", "min_intra_species_ani": "95.39", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900108305.1", "gtdb_species": "s__Nitrosomonas ureae_B", "ani": 78.03, "matched_fragments": 288, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "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_001455205.1", "gtdb_species": "s__Nitrosomonas ureae", "ani": 77.9991, "matched_fragments": 291, "total_fragments": 896, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Nitrosomonadaceae;g__Nitrosomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.016, "cell_length": 0.156, "doubling_h": 0.74, "growth_tmp": 27.75, "optimum_tmp": 27.2, "optimum_ph": 7.5, "genome_size": 3182652.593, "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, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Nitrosomonadaceae", "g__Nitrosomonas", "s__Nitrosomonas sp024282095" ], "_genome_taxon": [ "Nitrosomonas", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Gammaproteobacteria", "o__Burkholderiales", "f__Nitrosomonadaceae", "g__Nitrosomonas", "s__Nitrosomonas sp024282095", "Bacteria", "Pseudomonadota", "Gammaproteobacteria", "Burkholderiales", "Nitrosomonadaceae", "Nitrosomonas", "Nitrosomonas", "sp024282095" ], "_meo": [ { "id": "MEO_0000014", "label": "activated sludge" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }