{ "type": "genome", "identifier": "GCA_900760835.1", "organism": "Bacteroidaceae bacterium", "title": "Bacteroidaceae bacterium", "description": "derived from metagenome; genus undefined", "data type": "Genome sequencing and assembly", "organization": "DOE JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCA_900760835.1", "bioproject": "PRJEB31003", "biosample": "SAMEA5279614", "wgs_master": "CAAFAM000000000.1", "refseq_category": "na", "taxid": "2212467", "species_taxid": "2212467", "organism_name": "Bacteroidaceae bacterium", "infraspecific_name": "", "isolate": "HGM04768", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/26", "asm_name": "SRS022609_13", "submitter": "DOE JGI", "gbrs_paired_asm": "GCF_900760835.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/760/835/GCA_900760835.1_SRS022609_13", "excluded_from_refseq": "derived from metagenome; genus undefined", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-26", "dateModified": "2020-06-26", "datePublished": "2020-06-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Bacteroidaceae bacterium" ], "sample_taxid": [ "2212467" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.859 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 68.92, "contamination": 8.33, "strain_heterogeneity": 50.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2971789", "Number of Sequences": "529", "Longest Sequences (bp)": "60852", "N50 (bp)": "8567", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.1", "Number of CDSs": "1984", "Average Protein Length": "341.8", "Coding Ratio (%)": "68.5", "Number of rRNAs": "0", "Number of tRNAs": "30", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phocaeicola vulgatus", "strain": "strain=FDAARGOS_1098", "accession": "GCA_016766915.1", "taxid": 821, "species_taxid": 821, "relation_to_type": "type", "validated": true, "ani": 96.2649, "matched_fragments": 300, "total_fragments": 716, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Phocaeicola dorei", "strain": "strain=DSM 17855", "accession": "GCA_000156075.1", "taxid": 357276, "species_taxid": 357276, "relation_to_type": "type", "validated": true, "ani": 96.2422, "matched_fragments": 300, "total_fragments": 716, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Phocaeicola vulgatus", "strain": "strain=ATCC 8482", "accession": "GCA_000012825.1", "taxid": 821, "species_taxid": 821, "relation_to_type": "type", "validated": true, "ani": 96.2325, "matched_fragments": 302, "total_fragments": 716, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Phocaeicola dorei", "strain": "strain=DSM 17855", "accession": "GCA_025146415.1", "taxid": 357276, "species_taxid": 357276, "relation_to_type": "type", "validated": true, "ani": 96.198, "matched_fragments": 301, "total_fragments": 716, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Phocaeicola dorei", "strain": "strain=DSM 17855", "accession": "GCA_013009555.1", "taxid": 357276, "species_taxid": 357276, "relation_to_type": "type", "validated": true, "ani": 96.191, "matched_fragments": 302, "total_fragments": 716, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Bacteroides uniformis", "strain": "strain=ATCC 8492", "accession": "GCA_000154205.1", "taxid": 820, "species_taxid": 820, "relation_to_type": "type", "validated": true, "ani": 94.0448, "matched_fragments": 250, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides uniformis", "strain": "strain=DSM 6597", "accession": "GCA_900107315.1", "taxid": 820, "species_taxid": 820, "relation_to_type": "type", "validated": true, "ani": 93.9571, "matched_fragments": 251, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides uniformis", "strain": "strain=ATCC 8492", "accession": "GCA_025147485.1", "taxid": 820, "species_taxid": 820, "relation_to_type": "type", "validated": true, "ani": 93.9515, "matched_fragments": 248, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides uniformis", "strain": "strain=FDAARGOS_901", "accession": "GCA_016117815.1", "taxid": 820, "species_taxid": 820, "relation_to_type": "type", "validated": true, "ani": 93.9305, "matched_fragments": 257, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides humanifaecis", "strain": "strain=KGMB07931", "accession": "GCA_017309675.2", "taxid": 2792859, "species_taxid": 2792859, "relation_to_type": "type", "validated": true, "ani": 91.0855, "matched_fragments": 225, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides rodentium", "strain": "strain=JCM 16496", "accession": "GCA_000614125.1", "taxid": 691816, "species_taxid": 691816, "relation_to_type": "type", "validated": true, "ani": 89.9993, "matched_fragments": 208, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola sartorii", "strain": "strain=DSM 21941", "accession": "GCA_024622025.1", "taxid": 671267, "species_taxid": 671267, "relation_to_type": "type", "validated": true, "ani": 88.9053, "matched_fragments": 261, "total_fragments": 716, "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": 80.0, "matched_fragments": 116, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides eggerthii", "strain": "strain=DSM 20697", "accession": "GCA_025146565.1", "taxid": 28111, "species_taxid": 28111, "relation_to_type": "type", "validated": true, "ani": 79.8888, "matched_fragments": 109, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides thetaiotaomicron", "strain": "strain=VPI 5482", "accession": "GCA_022453665.1", "taxid": 818, "species_taxid": 818, "relation_to_type": "type", "validated": true, "ani": 78.4565, "matched_fragments": 85, "total_fragments": 716, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 68.92, "contamination": 8.33, "strain_heterogeneity": 50.0 }, "gtdb_result": [ { "accession": "GCF_000012825.1", "gtdb_species": "s__Phocaeicola vulgatus", "ani": 96.2325, "matched_fragments": 302, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.359, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "95.43", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.61", "num_clustered_genomes": 263, "status": "inconclusive" }, { "accession": "GCF_013009555.1", "gtdb_species": "s__Phocaeicola dorei", "ani": 96.191, "matched_fragments": 302, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.359, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "97.27", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.54", "num_clustered_genomes": 104, "status": "inconclusive" }, { "accession": "GCA_900760795.1", "gtdb_species": "s__Phocaeicola sp900760795", "ani": 94.4043, "matched_fragments": 235, "total_fragments": 716, "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": "GCF_000154205.1", "gtdb_species": "s__Bacteroides uniformis", "ani": 94.046, "matched_fragments": 250, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "95.87", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.69", "num_clustered_genomes": 301, "status": "-" }, { "accession": "GCF_000614125.1", "gtdb_species": "s__Bacteroides rodentium", "ani": 90.0546, "matched_fragments": 207, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "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_004793475.1", "gtdb_species": "s__Bacteroides sp002491635", "ani": 89.4687, "matched_fragments": 197, "total_fragments": 716, "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": "-" }, { "accession": "GCA_011959205.1", "gtdb_species": "s__Phocaeicola sp011959205", "ani": 88.8677, "matched_fragments": 219, "total_fragments": 716, "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": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000614185.1", "gtdb_species": "s__Phocaeicola sartorii", "ani": 88.7834, "matched_fragments": 256, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.44", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.76", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000195635.1", "gtdb_species": "s__Bacteroides fluxus", "ani": 80.619, "matched_fragments": 152, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.66", "min_intra_species_ani": "99.32", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_905203765.1", "gtdb_species": "s__Bacteroides sp905203765", "ani": 80.1239, "matched_fragments": 84, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "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_902388495.1", "gtdb_species": "s__Bacteroides sp902388495", "ani": 79.9698, "matched_fragments": 160, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003438615.1", "gtdb_species": "s__Bacteroides sp003545565", "ani": 79.7221, "matched_fragments": 110, "total_fragments": 716, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.56", "min_intra_species_ani": "99.02", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 7, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.149, "cell_length": 0.21, "doubling_h": -0.095, "growth_tmp": 36.675, "optimum_tmp": 36.026, "optimum_ph": 6.997, "genome_size": 4766044.241, "gc_content": 43.414, "coding_genes": 3969.717, "rRNA16S_genes": 5.5, "tRNA_genes": 71.066, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Phocaeicola", "s__" ], "_genome_taxon": [ "Bacteroidaceae", "bacterium", "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Phocaeicola", "s__", "Bacteria", "Bacteroidota", "Bacteroidia", "Bacteroidales", "Bacteroidaceae", "Phocaeicola", "s", "", "" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }