{ "type": "genome", "identifier": "GCA_934692435.1", "organism": "uncultured Phocaeicola sp.", "title": "uncultured Phocaeicola sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "stanford university school of medicine", "publication": [ {} ], "properties": { "assembly_accession": "GCA_934692435.1", "bioproject": "PRJEB49206", "biosample": "SAMEA13522012", "wgs_master": "CAKUTV000000000.1", "refseq_category": "na", "taxid": "990718", "species_taxid": "990718", "organism_name": "uncultured Phocaeicola sp.", "infraspecific_name": "", "isolate": "REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_J_6_2308.13", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/04/16", "asm_name": "ERR7747782_bin.13", "submitter": "stanford university school of medicine", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/934/692/435/GCA_934692435.1_ERR7747782_bin.13", "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": "2022-04-16", "dateModified": "2022-04-16", "datePublished": "2022-04-16", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Phocaeicola sp." ], "sample_taxid": [ "990718" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Tanzania" ], "sample_host_location_id": [], "data_size": "0.986 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)": "3414828", "Number of Sequences": "90", "Longest Sequences (bp)": "166914", "N50 (bp)": "70697", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.0", "Number of CDSs": "2556", "Average Protein Length": "395.3", "Coding Ratio (%)": "88.8", "Number of rRNAs": "0", "Number of tRNAs": "55", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phocaeicola coprocola", "strain": "strain=DSM 17136", "accession": "GCA_000154845.1", "taxid": 310298, "species_taxid": 310298, "relation_to_type": "suspected-type", "validated": true, "ani": 79.4365, "matched_fragments": 239, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola plebeius", "strain": "strain=DSM 17135", "accession": "GCA_000187895.1", "taxid": 310297, "species_taxid": 310297, "relation_to_type": "suspected-type", "validated": true, "ani": 79.3906, "matched_fragments": 220, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola faecicola", "strain": "strain=AGMB03916", "accession": "GCA_013618865.1", "taxid": 2739389, "species_taxid": 2739389, "relation_to_type": "type", "validated": true, "ani": 79.0655, "matched_fragments": 220, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola coprophilus", "strain": "strain=JCM 13818", "accession": "GCA_001315785.1", "taxid": 387090, "species_taxid": 387090, "relation_to_type": "type", "validated": true, "ani": 78.8564, "matched_fragments": 176, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola coprophilus", "strain": "strain=DSM 18228", "accession": "GCA_000157915.1", "taxid": 387090, "species_taxid": 387090, "relation_to_type": "type", "validated": true, "ani": 78.7274, "matched_fragments": 184, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola barnesiae", "strain": "strain=JCM 13652", "accession": "GCA_000613645.1", "taxid": 376804, "species_taxid": 376804, "relation_to_type": "type", "validated": true, "ani": 78.6616, "matched_fragments": 220, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola barnesiae", "strain": "strain=DSM 18169", "accession": "GCA_000374585.1", "taxid": 376804, "species_taxid": 376804, "relation_to_type": "type", "validated": true, "ani": 78.5925, "matched_fragments": 220, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides caccae", "strain": "strain=ATCC 43185", "accession": "GCA_025146315.1", "taxid": 47678, "species_taxid": 47678, "relation_to_type": "suspected-type", "validated": true, "ani": 77.7334, "matched_fragments": 116, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides stercorirosoris", "strain": "strain=JCM 17103", "accession": "GCA_000614165.1", "taxid": 871324, "species_taxid": 871324, "relation_to_type": "type", "validated": true, "ani": 77.7318, "matched_fragments": 113, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides ovatus", "strain": "strain=ATCC 8483", "accession": "GCA_001314995.1", "taxid": 28116, "species_taxid": 28116, "relation_to_type": "suspected-type", "validated": true, "ani": 77.6105, "matched_fragments": 127, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides propionicigenes", "strain": "strain=NSJ-90", "accession": "GCA_018390535.1", "taxid": 2834112, "species_taxid": 2834112, "relation_to_type": "type", "validated": true, "ani": 77.575, "matched_fragments": 126, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides muris", "strain": "strain=KH365_2", "accession": "GCA_024704915.1", "taxid": 2937417, "species_taxid": 2937417, "relation_to_type": "type", "validated": true, "ani": 77.5242, "matched_fragments": 102, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola salanitronis", "strain": "strain=DSM 18170", "accession": "GCA_000190575.1", "taxid": 376805, "species_taxid": 376805, "relation_to_type": "type", "validated": true, "ani": 77.5153, "matched_fragments": 189, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides ovatus", "strain": "strain=NCTC11153", "accession": "GCA_900445505.1", "taxid": 28116, "species_taxid": 28116, "relation_to_type": "suspected-type", "validated": true, "ani": 77.515, "matched_fragments": 125, "total_fragments": 1090, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_000434735.1", "gtdb_species": "s__Phocaeicola sp000434735", "ani": 95.6698, "matched_fragments": 888, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.56", "min_intra_species_ani": "97.52", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.81", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000154845.1", "gtdb_species": "s__Phocaeicola coprocola", "ani": 79.4397, "matched_fragments": 238, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.02", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.65", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_000187895.1", "gtdb_species": "s__Phocaeicola plebeius", "ani": 79.3694, "matched_fragments": 221, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.22", "min_intra_species_ani": "96.70", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.55", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_003437535.1", "gtdb_species": "s__Phocaeicola plebeius_A", "ani": 79.1701, "matched_fragments": 223, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "95.85", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.73", "num_clustered_genomes": 27, "status": "-" }, { "accession": "GCF_013618865.1", "gtdb_species": "s__Phocaeicola sp900541515", "ani": 79.093, "matched_fragments": 218, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "99.22", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_016900355.1", "gtdb_species": "s__Phocaeicola sp900551065", "ani": 79.0751, "matched_fragments": 205, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.34", "min_intra_species_ani": "95.04", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900128455.1", "gtdb_species": "s__Phocaeicola mediterraneensis", "ani": 78.9937, "matched_fragments": 195, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.66", "min_intra_species_ani": "98.61", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.80", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900128495.1", "gtdb_species": "s__Phocaeicola ilei", "ani": 78.8386, "matched_fragments": 182, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000157915.1", "gtdb_species": "s__Phocaeicola coprophilus", "ani": 78.7271, "matched_fragments": 184, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.31", "min_intra_species_ani": "98.55", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.87", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_000432735.1", "gtdb_species": "s__Phocaeicola sp000432735", "ani": 78.6755, "matched_fragments": 235, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016902295.1", "gtdb_species": "s__Phocaeicola caecigallinarum_A", "ani": 78.6456, "matched_fragments": 188, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "97.48", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.83", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902362595.1", "gtdb_species": "s__Phocaeicola merdigallinarum", "ani": 78.508, "matched_fragments": 218, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "96.40", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.80", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_900542985.1", "gtdb_species": "s__Phocaeicola sp900542985", "ani": 78.4462, "matched_fragments": 185, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.57", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.72", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900552075.1", "gtdb_species": "s__Phocaeicola sp900552075", "ani": 78.3106, "matched_fragments": 154, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "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_000436795.1", "gtdb_species": "s__Phocaeicola sp000436795", "ani": 78.0156, "matched_fragments": 197, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.87", "min_intra_species_ani": "99.87", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_004793475.1", "gtdb_species": "s__Bacteroides sp002491635", "ani": 77.3656, "matched_fragments": 110, "total_fragments": 1090, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.51", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.83", "num_clustered_genomes": 13, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": -0.523, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2530631.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "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": 0.0, "coccus_cell_shape": 1.0, "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__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Phocaeicola", "s__Phocaeicola sp000434735" ], "_genome_taxon": [ "uncultured", "Phocaeicola", "sp.", "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Phocaeicola", "s__Phocaeicola sp000434735", "Bacteria", "Bacteroidota", "Bacteroidia", "Bacteroidales", "Bacteroidaceae", "Phocaeicola", "Phocaeicola", "sp000434735" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }