{ "type": "genome", "identifier": "GCA_027310345.1", "organism": "Nitrospira sp.", "title": "Nitrospira sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "an eLibrary of Microbial Systematics and Genomics", "publication": [ {} ], "properties": { "assembly_accession": "GCA_027310345.1", "bioproject": "PRJNA834572", "biosample": "SAMN28081205", "wgs_master": "DAIDBA000000000.1", "refseq_category": "na", "taxid": "70125", "species_taxid": "70125", "organism_name": "Nitrospira sp.", "infraspecific_name": "", "isolate": "clean1854", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/12/27", "asm_name": "ASM2731034v1", "submitter": "an eLibrary of Microbial Systematics and Genomics", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/027/310/345/GCA_027310345.1_ASM2731034v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-12-27", "dateModified": "2022-12-27", "datePublished": "2022-12-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Nitrospira sp." ], "sample_taxid": [ "70125" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Brazil: Canaa dos Carajas" ], "sample_host_location_id": [], "data_size": "0.710 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 52.46, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2428469", "Number of Sequences": "834", "Longest Sequences (bp)": "23694", "N50 (bp)": "3006", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.2", "Number of CDSs": "1824", "Average Protein Length": "223.4", "Coding Ratio (%)": "50.3", "Number of rRNAs": "0", "Number of tRNAs": "20", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [], "cc_result": { "completeness": 52.46, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_018242765.1", "gtdb_species": "s__Nitrospira_F sp018242765", "ani": 78.7267, "matched_fragments": 81, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.34", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_902500775.1", "gtdb_species": "s__Nitrospira_F sp902500775", "ani": 78.2755, "matched_fragments": 71, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "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_002254365.1", "gtdb_species": "s__Nitrospira_F sp002254365", "ani": 78.2243, "matched_fragments": 74, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.98", "min_intra_species_ani": "97.05", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.74", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001458735.1", "gtdb_species": "s__Nitrospira_F nitrosa", "ani": 78.195, "matched_fragments": 75, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.74", "min_intra_species_ani": "95.74", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.79", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_011331925.1", "gtdb_species": "s__Nitrospira_F sp011331925", "ani": 78.1548, "matched_fragments": 80, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "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_018242725.1", "gtdb_species": "s__Nitrospira_F sp018242725", "ani": 77.8526, "matched_fragments": 74, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "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_005116965.1", "gtdb_species": "s__Nitrospira_F sp005116965", "ani": 77.8461, "matched_fragments": 74, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.63", "min_intra_species_ani": "96.63", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002083365.1", "gtdb_species": "s__Nitrospira_F sp002083365", "ani": 77.7209, "matched_fragments": 93, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "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_014058405.1", "gtdb_species": "s__Nitrospira_F kreftii", "ani": 77.6567, "matched_fragments": 51, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "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_900696515.1", "gtdb_species": "s__Nitrospira_F sp900696515", "ani": 77.5879, "matched_fragments": 68, "total_fragments": 319, "gtdb_taxonomy": "d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.74", "min_intra_species_ani": "97.08", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.77", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.388, "cell_length": null, "doubling_h": 1.079, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": 4195141.429, "gc_content": 59.803, "coding_genes": 3920.25, "rRNA16S_genes": 1.0, "tRNA_genes": 46.5, "gram_stain": 0.0, "sporulation": 0.0, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": 0.0, "vibrio_cell_shape": 1.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Nitrospirota", "c__Nitrospiria", "o__Nitrospirales", "f__Nitrospiraceae", "g__Nitrospira_D", "s__" ], "_genome_taxon": [ "Nitrospira", "sp.", "d__Bacteria", "p__Nitrospirota", "c__Nitrospiria", "o__Nitrospirales", "f__Nitrospiraceae", "g__Nitrospira_D", "s__", "Bacteria", "Nitrospirota", "Nitrospiria", "Nitrospirales", "Nitrospiraceae", "Nitrospira", "D", "s", "", "" ], "_meo": [ { "id": "MEO_0000034", "label": "acid mine drainage" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }