{ "type": "genome", "identifier": "GCA_900764875.1", "organism": "uncultured Bacteroides sp.", "title": "uncultured Bacteroides sp.", "description": "derived from environmental source; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "DOE JGI", "publication": [ {} ], "properties": { "assembly_accession": "GCA_900764875.1", "bioproject": "PRJEB31003", "biosample": "SAMEA5278514", "wgs_master": "CAAFPM000000000.1", "refseq_category": "na", "taxid": "162156", "species_taxid": "162156", "organism_name": "uncultured Bacteroides sp.", "infraspecific_name": "", "isolate": "HGM04662", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/25", "asm_name": "SRS259467_2", "submitter": "DOE JGI", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/764/875/GCA_900764875.1_SRS259467_2", "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": "2020-06-25", "dateModified": "2020-06-25", "datePublished": "2020-06-25", "_annotation": { "sample_count": 1, "sample_organism": [ "uncultured Bacteroides sp." ], "sample_taxid": [ "162156" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.780 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 50.0, "contamination": 4.17, "strain_heterogeneity": 100.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2702680", "Number of Sequences": "269", "Longest Sequences (bp)": "101392", "N50 (bp)": "20103", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "45.4", "Number of CDSs": "1917", "Average Protein Length": "383.9", "Coding Ratio (%)": "81.7", "Number of rRNAs": "0", "Number of tRNAs": "6", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bacteroides eggerthii", "strain": "strain=DSM 20697", "accession": "GCA_025146565.1", "taxid": 28111, "species_taxid": 28111, "relation_to_type": "type", "validated": true, "ani": 94.6722, "matched_fragments": 405, "total_fragments": 769, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides eggerthii", "strain": "strain=DSM 20697", "accession": "GCA_000155815.1", "taxid": 28111, "species_taxid": 28111, "relation_to_type": "type", "validated": true, "ani": 94.5229, "matched_fragments": 409, "total_fragments": 769, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides eggerthii", "strain": "strain=NCTC11155", "accession": "GCA_900445565.1", "taxid": 28111, "species_taxid": 28111, "relation_to_type": "type", "validated": true, "ani": 94.4865, "matched_fragments": 406, "total_fragments": 769, "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": 93.8584, "matched_fragments": 438, "total_fragments": 769, "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": 93.858, "matched_fragments": 433, "total_fragments": 769, "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": 93.7048, "matched_fragments": 444, "total_fragments": 769, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides uniformis", "strain": "strain=ATCC 8492", "accession": "GCA_000154205.1", "taxid": 820, "species_taxid": 820, "relation_to_type": "type", "validated": true, "ani": 93.6984, "matched_fragments": 440, "total_fragments": 769, "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": 91.501, "matched_fragments": 403, "total_fragments": 769, "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": 88.863, "matched_fragments": 347, "total_fragments": 769, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides clarus", "strain": "strain=YIT 12056", "accession": "GCA_000195615.1", "taxid": 626929, "species_taxid": 626929, "relation_to_type": "type", "validated": true, "ani": 83.5278, "matched_fragments": 304, "total_fragments": 769, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides clarus", "strain": "strain=YIT 12056", "accession": "GCA_900129655.1", "taxid": 626929, "species_taxid": 626929, "relation_to_type": "type", "validated": true, "ani": 83.4586, "matched_fragments": 310, "total_fragments": 769, "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": 83.1084, "matched_fragments": 335, "total_fragments": 769, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides stercoris", "strain": "strain=ATCC 43183", "accession": "GCA_025147325.1", "taxid": 46506, "species_taxid": 46506, "relation_to_type": "suspected-type", "validated": true, "ani": 82.7678, "matched_fragments": 312, "total_fragments": 769, "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": 79.1988, "matched_fragments": 245, "total_fragments": 769, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 50.0, "contamination": 4.17, "strain_heterogeneity": 100.0 }, "gtdb_result": [ { "accession": "GCF_000155815.1", "gtdb_species": "s__Bacteroides eggerthii", "ani": 94.5229, "matched_fragments": 409, "total_fragments": 769, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.86", "min_intra_species_ani": "98.28", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.74", "num_clustered_genomes": 51, "status": "-" }, { "accession": "GCF_000154205.1", "gtdb_species": "s__Bacteroides uniformis", "ani": 93.655, "matched_fragments": 441, "total_fragments": 769, "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": 89.6228, "matched_fragments": 372, "total_fragments": 769, "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": 88.1943, "matched_fragments": 346, "total_fragments": 769, "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_905197435.1", "gtdb_species": "s__Bacteroides sp905197435", "ani": 85.7172, "matched_fragments": 268, "total_fragments": 769, "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_900129655.1", "gtdb_species": "s__Bacteroides clarus", "ani": 83.488, "matched_fragments": 309, "total_fragments": 769, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.47", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.82", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_003438615.1", "gtdb_species": "s__Bacteroides sp003545565", "ani": 83.1032, "matched_fragments": 334, "total_fragments": 769, "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": "-" }, { "accession": "GCF_000154525.1", "gtdb_species": "s__Bacteroides stercoris", "ani": 82.7763, "matched_fragments": 321, "total_fragments": 769, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.69", "num_clustered_genomes": 73, "status": "-" }, { "accession": "GCF_000374365.1", "gtdb_species": "s__Bacteroides gallinarum", "ani": 81.4598, "matched_fragments": 308, "total_fragments": 769, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_902388495.1", "gtdb_species": "s__Bacteroides sp902388495", "ani": 80.3369, "matched_fragments": 273, "total_fragments": 769, "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_000195635.1", "gtdb_species": "s__Bacteroides fluxus", "ani": 80.1695, "matched_fragments": 284, "total_fragments": 769, "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": "GCF_000186225.1", "gtdb_species": "s__Bacteroides helcogenes", "ani": 79.2126, "matched_fragments": 232, "total_fragments": 769, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.136, "cell_length": 0.217, "doubling_h": -0.095, "growth_tmp": 36.666, "optimum_tmp": 36.026, "optimum_ph": 6.997, "genome_size": 4818468.536, "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__Bacteroides", "s__" ], "_genome_taxon": [ "uncultured", "Bacteroides", "sp.", "d__Bacteria", "p__Bacteroidota", "c__Bacteroidia", "o__Bacteroidales", "f__Bacteroidaceae", "g__Bacteroides", "s__", "Bacteria", "Bacteroidota", "Bacteroidia", "Bacteroidales", "Bacteroidaceae", "Bacteroides", "s", "", "" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }