{ "type": "genome", "identifier": "GCA_903913215.1", "organism": "uncultured Holophagaceae bacterium", "title": "uncultured Holophagaceae bacterium", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "BILS", "publication": [ {} ], "properties": { "assembly_accession": "GCA_903913215.1", "bioproject": "PRJEB38681", "biosample": "SAMEA6954206", "wgs_master": "CAIWKE000000000.1", "refseq_category": "na", "taxid": "904990", "species_taxid": "904990", "organism_name": "uncultured Holophagaceae bacterium", "infraspecific_name": "", "isolate": "A14_bin-1248", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/19", "asm_name": "freshwater MAG --- A14_bin-1248", "submitter": "BILS", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/913/215/GCA_903913215.1_freshwater_MAG_---_A14_bin-1248", "excluded_from_refseq": "derived from environmental source; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-19", "dateModified": "2020-07-19", "datePublished": "2020-07-19", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Holophagaceae bacterium" ], "sample_taxid": [ "904990" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada" ], "sample_host_location_id": [], "data_size": "1.084 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "3902199", "Number of Sequences": "41", "Longest Sequences (bp)": "476166", "N50 (bp)": "159703", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.0", "Number of CDSs": "3434", "Average Protein Length": "338.7", "Coding Ratio (%)": "89.4", "Number of rRNAs": "0", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Geothrix fermentans", "strain": "strain=DSM 14018", "accession": "GCA_000428885.1", "taxid": 44676, "species_taxid": 44676, "relation_to_type": "type", "validated": true, "ani": 83.1013, "matched_fragments": 689, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Holophaga foetida", "strain": "strain=DSM 6591", "accession": "GCA_000242615.3", "taxid": 35839, "species_taxid": 35839, "relation_to_type": "type", "validated": true, "ani": 77.979, "matched_fragments": 265, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Inmirania thermothiophila", "strain": "strain=DSM 100275", "accession": "GCA_003751635.1", "taxid": 1750597, "species_taxid": 1750597, "relation_to_type": "type", "validated": true, "ani": 75.4699, "matched_fragments": 57, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Azospira oryzae", "strain": "strain=DSM 21223", "accession": "GCA_004217225.1", "taxid": 146939, "species_taxid": 146939, "relation_to_type": "type", "validated": true, "ani": 75.2914, "matched_fragments": 94, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ramlibacter aquaticus", "strain": "strain=LMG 30558", "accession": "GCA_015159745.1", "taxid": 2780094, "species_taxid": 2780094, "relation_to_type": "type", "validated": true, "ani": 75.2471, "matched_fragments": 85, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thioalkalivibrio sulfidiphilus", "strain": "strain=HL-EbGR7", "accession": "GCA_000021985.1", "taxid": 1033854, "species_taxid": 1033854, "relation_to_type": "type", "validated": true, "ani": 75.2329, "matched_fragments": 59, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hypericibacter terrae", "strain": "strain=R5913", "accession": "GCA_008728855.1", "taxid": 2602015, "species_taxid": 2602015, "relation_to_type": "type", "validated": true, "ani": 74.9291, "matched_fragments": 52, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptomyces spirodelae", "strain": "strain=DW4-2", "accession": "GCA_017676385.1", "taxid": 2812904, "species_taxid": 2812904, "relation_to_type": "type", "validated": true, "ani": 74.6797, "matched_fragments": 57, "total_fragments": 1279, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 79.17, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903913215.1", "gtdb_species": "s__Geothrix sp903913215", "ani": 100.0, "matched_fragments": 1277, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "97.99", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 29, "status": "conclusive" }, { "accession": "GCA_013390615.1", "gtdb_species": "s__Geothrix sp013390615", "ani": 83.2579, "matched_fragments": 772, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "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_016714685.1", "gtdb_species": "s__Geothrix sp016714685", "ani": 83.1957, "matched_fragments": 725, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.39", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000428885.1", "gtdb_species": "s__Geothrix fermentans", "ani": 83.1014, "matched_fragments": 689, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "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_013334395.1", "gtdb_species": "s__Geothrix sp013334395", "ani": 82.9682, "matched_fragments": 612, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "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_903857495.1", "gtdb_species": "s__Geothrix sp903857495", "ani": 82.8748, "matched_fragments": 763, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.98", "num_clustered_genomes": 50, "status": "-" }, { "accession": "GCA_003538615.1", "gtdb_species": "s__Geothrix sp003538615", "ani": 82.8637, "matched_fragments": 529, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "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_903937385.1", "gtdb_species": "s__Geothrix sp903937385", "ani": 82.834, "matched_fragments": 751, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "98.90", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_016721195.1", "gtdb_species": "s__Geothrix sp016721195", "ani": 82.727, "matched_fragments": 752, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "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_903840385.1", "gtdb_species": "s__Geothrix sp903840385", "ani": 82.118, "matched_fragments": 606, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.80", "min_intra_species_ani": "99.80", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_016195985.1", "gtdb_species": "s__Geothrix sp016195985", "ani": 82.0956, "matched_fragments": 723, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_903843705.1", "gtdb_species": "s__Geothrix sp903843705", "ani": 82.0932, "matched_fragments": 648, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "98.86", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_903876615.1", "gtdb_species": "s__Geothrix sp903876615", "ani": 81.4013, "matched_fragments": 413, "total_fragments": 1279, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "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": -1.0, "cell_length": 0.0, "doubling_h": null, "growth_tmp": 31.5, "optimum_tmp": 32.5, "optimum_ph": 7.15, "genome_size": 3708525.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Acidobacteriota", "c__Holophagae", "o__Holophagales", "f__Holophagaceae", "g__Geothrix", "s__Geothrix sp903913215" ], "_genome_taxon": [ "uncultured", "Holophagaceae", "bacterium", "d__Bacteria", "p__Acidobacteriota", "c__Holophagae", "o__Holophagales", "f__Holophagaceae", "g__Geothrix", "s__Geothrix sp903913215", "Bacteria", "Acidobacteriota", "Holophagae", "Holophagales", "Holophagaceae", "Geothrix", "Geothrix", "sp903913215" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000027", "label": "pond" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }