{ "type": "genome", "identifier": "GCA_903893705.1", "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_903893705.1", "bioproject": "PRJEB38681", "biosample": "SAMEA6954982", "wgs_master": "CAITNH000000000.1", "refseq_category": "na", "taxid": "904990", "species_taxid": "904990", "organism_name": "uncultured Holophagaceae bacterium", "infraspecific_name": "", "isolate": "MJ_bin-0908", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/19", "asm_name": "freshwater MAG --- MJ_bin-0908", "submitter": "BILS", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/903/893/705/GCA_903893705.1_freshwater_MAG_---_MJ_bin-0908", "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": [ "Finland" ], "sample_host_location_id": [], "data_size": "0.988 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)": "3606621", "Number of Sequences": "55", "Longest Sequences (bp)": "273117", "N50 (bp)": "98650", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "67.8", "Number of CDSs": "3117", "Average Protein Length": "348.8", "Coding Ratio (%)": "90.4", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "3" }, "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": 84.0921, "matched_fragments": 716, "total_fragments": 1174, "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": 78.3792, "matched_fragments": 289, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga borbori", "strain": "strain=LA-38", "accession": "GCA_003417535.1", "taxid": 2294117, "species_taxid": 2294117, "relation_to_type": "type", "validated": true, "ani": 75.5273, "matched_fragments": 92, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga crocea", "strain": "strain=BA0156", "accession": "GCA_011388215.1", "taxid": 2716225, "species_taxid": 2716225, "relation_to_type": "type", "validated": true, "ani": 75.5072, "matched_fragments": 102, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Thermithiobacillus tepidarius", "strain": "strain=DSM 3134", "accession": "GCA_000423825.1", "taxid": 929, "species_taxid": 929, "relation_to_type": "type", "validated": true, "ani": 75.4963, "matched_fragments": 64, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Castellaniella defragrans", "strain": "strain=CCUG 39790", "accession": "GCA_008801975.1", "taxid": 75697, "species_taxid": 75697, "relation_to_type": "type", "validated": true, "ani": 75.4604, "matched_fragments": 94, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Castellaniella defragrans", "strain": "strain=DSM 12141", "accession": "GCA_014203015.1", "taxid": 75697, "species_taxid": 75697, "relation_to_type": "type", "validated": true, "ani": 75.4046, "matched_fragments": 100, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Comamonas terrae", "strain": "strain=NBRC 106524", "accession": "GCA_001544075.1", "taxid": 673548, "species_taxid": 673548, "relation_to_type": "type", "validated": true, "ani": 75.3972, "matched_fragments": 81, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Acidovorax wautersii", "strain": "strain=DSM 27981", "accession": "GCA_900113035.1", "taxid": 1177982, "species_taxid": 1177982, "relation_to_type": "type", "validated": true, "ani": 75.3281, "matched_fragments": 117, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stigmatella erecta", "strain": "strain=DSM 16858", "accession": "GCA_900111745.1", "taxid": 83460, "species_taxid": 83460, "relation_to_type": "type", "validated": true, "ani": 75.3004, "matched_fragments": 141, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stigmatella hybrida", "strain": "strain=DSM 14722", "accession": "GCA_020103775.1", "taxid": 394097, "species_taxid": 394097, "relation_to_type": "type", "validated": true, "ani": 75.1311, "matched_fragments": 143, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stigmatella aurantiaca", "strain": "strain=DSM 17044", "accession": "GCA_900109545.1", "taxid": 41, "species_taxid": 41, "relation_to_type": "type", "validated": true, "ani": 75.1277, "matched_fragments": 154, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavonifractor plautii", "strain": "strain=JCM 32125", "accession": "GCA_010508875.1", "taxid": 292800, "species_taxid": 292800, "relation_to_type": "suspected-type", "validated": true, "ani": 75.0309, "matched_fragments": 51, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Flavonifractor plautii", "strain": "strain=ATCC 29863", "accession": "GCA_000239295.1", "taxid": 292800, "species_taxid": 292800, "relation_to_type": "suspected-type", "validated": true, "ani": 75.0189, "matched_fragments": 52, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix tamanrassetensis", "strain": "strain=CECT 8640", "accession": "GCA_014203665.1", "taxid": 1051531, "species_taxid": 1051531, "relation_to_type": "type", "validated": true, "ani": 74.9931, "matched_fragments": 95, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Saccharothrix australiensis", "strain": "strain=DSM 43800", "accession": "GCA_003634935.1", "taxid": 2072, "species_taxid": 2072, "relation_to_type": "type", "validated": true, "ani": 74.9654, "matched_fragments": 96, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium pekingense", "strain": "strain=DSM 21552", "accession": "GCA_000421185.1", "taxid": 384677, "species_taxid": 384677, "relation_to_type": "type", "validated": true, "ani": 74.9536, "matched_fragments": 70, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Ornithinimicrobium pekingense", "strain": "strain=CGMCC 1.5362", "accession": "GCA_014644955.1", "taxid": 384677, "species_taxid": 384677, "relation_to_type": "type", "validated": true, "ani": 74.9536, "matched_fragments": 70, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kocuria dechangensis", "strain": "strain=CGMCC 1.12187", "accession": "GCA_014636775.1", "taxid": 1176249, "species_taxid": 1176249, "relation_to_type": "type", "validated": true, "ani": 74.8536, "matched_fragments": 82, "total_fragments": 1174, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_903857495.1", "gtdb_species": "s__Geothrix sp903857495", "ani": 99.9928, "matched_fragments": 1157, "total_fragments": 1174, "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": "conclusive" }, { "accession": "GCA_903863195.1", "gtdb_species": "s__Geothrix sp903863195", "ani": 94.2347, "matched_fragments": 918, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.63", "min_intra_species_ani": "99.47", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_903937385.1", "gtdb_species": "s__Geothrix sp903937385", "ani": 93.7401, "matched_fragments": 1021, "total_fragments": 1174, "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_013334395.1", "gtdb_species": "s__Geothrix sp013334395", "ani": 92.2229, "matched_fragments": 769, "total_fragments": 1174, "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_903843705.1", "gtdb_species": "s__Geothrix sp903843705", "ani": 90.9664, "matched_fragments": 860, "total_fragments": 1174, "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": 90.2984, "matched_fragments": 541, "total_fragments": 1174, "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_903890595.1", "gtdb_species": "s__Geothrix sp903890595", "ani": 84.874, "matched_fragments": 608, "total_fragments": 1174, "gtdb_taxonomy": "d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.18", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.81", "num_clustered_genomes": 6, "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 sp903857495" ], "_genome_taxon": [ "uncultured", "Holophagaceae", "bacterium", "d__Bacteria", "p__Acidobacteriota", "c__Holophagae", "o__Holophagales", "f__Holophagaceae", "g__Geothrix", "s__Geothrix sp903857495", "Bacteria", "Acidobacteriota", "Holophagae", "Holophagales", "Holophagaceae", "Geothrix", "Geothrix", "sp903857495" ], "_meo": [ { "id": "MEO_0000038", "label": "freshwater" }, { "id": "MEO_0000024", "label": "lake" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }