{ "type": "genome", "identifier": "GCF_900129065.1", "organism": "Bacteroides faecichinchillae", "title": "Bacteroides faecichinchillae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900129065.1", "bioproject": "PRJNA224116", "biosample": "SAMN05444349", "wgs_master": "FQVD00000000.1", "refseq_category": "reference genome", "taxid": "871325", "species_taxid": "871325", "organism_name": "Bacteroides faecichinchillae", "infraspecific_name": "strain=DSM 26883", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/03", "asm_name": "IMG-taxon 2695420934 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900129065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/129/065/GCF_900129065.1_IMG-taxon_2695420934_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4806522", "genome_size_ungapped": "4806522", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "88", "contig_count": "88", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900129065.1-RS_2024_10_22", "annotation_date": "2024-10-22", "total_gene_count": "4060", "protein_coding_gene_count": "3839", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-03", "dateModified": "2016-12-03", "datePublished": "2016-12-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Bacteroides faecichinchillae" ], "sample_taxid": [ "871325" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.368 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": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4806522", "Number of Sequences": "88", "Longest Sequences (bp)": "320720", "N50 (bp)": "133019", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.7", "Number of CDSs": "3884", "Average Protein Length": "353.0", "Coding Ratio (%)": "85.6", "Number of rRNAs": "3", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bacteroides faecichinchillae", "strain": "strain=DSM 26883", "accession": "GCA_900129065.1", "taxid": 871325, "species_taxid": 871325, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1551, "total_fragments": 1557, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bacteroides faecichinchillae", "strain": "strain=JCM 17102", "accession": "GCA_000614145.1", "taxid": 871325, "species_taxid": 871325, "relation_to_type": "type", "validated": true, "ani": 99.9501, "matched_fragments": 1497, "total_fragments": 1557, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bacteroides bouchesdurhonensis", "strain": "strain=Marseille-P2653", "accession": "GCA_900155865.1", "taxid": 1841855, "species_taxid": 1841855, "relation_to_type": "type", "validated": true, "ani": 94.4727, "matched_fragments": 1223, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides faecalis", "strain": "strain=KCTC 15687", "accession": "GCA_003865075.1", "taxid": 2447885, "species_taxid": 2447885, "relation_to_type": "type", "validated": true, "ani": 93.7541, "matched_fragments": 1238, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides caecimuris", "strain": "strain=I48", "accession": "GCA_016697125.1", "taxid": 1796613, "species_taxid": 1796613, "relation_to_type": "type", "validated": true, "ani": 81.2347, "matched_fragments": 557, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides caecimuris", "strain": "strain=I48", "accession": "GCA_023277905.1", "taxid": 1796613, "species_taxid": 1796613, "relation_to_type": "type", "validated": true, "ani": 81.1239, "matched_fragments": 567, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides ovatus", "strain": "strain=FDAARGOS_1516", "accession": "GCA_020149745.1", "taxid": 28116, "species_taxid": 28116, "relation_to_type": "suspected-type", "validated": true, "ani": 80.7212, "matched_fragments": 623, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides ovatus", "strain": "strain=ATCC 8483", "accession": "GCA_025146775.1", "taxid": 28116, "species_taxid": 28116, "relation_to_type": "suspected-type", "validated": true, "ani": 80.7041, "matched_fragments": 623, "total_fragments": 1557, "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": 80.7002, "matched_fragments": 629, "total_fragments": 1557, "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": 79.9912, "matched_fragments": 613, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides luhongzhouii", "strain": "strain=HF-5141", "accession": "GCA_009193295.2", "taxid": 2650158, "species_taxid": 2650158, "relation_to_type": "type", "validated": true, "ani": 79.8536, "matched_fragments": 582, "total_fragments": 1557, "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": 79.3969, "matched_fragments": 256, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides nordii", "strain": "strain=FDAARGOS_1461", "accession": "GCA_019930665.1", "taxid": 291645, "species_taxid": 291645, "relation_to_type": "type", "validated": true, "ani": 79.2309, "matched_fragments": 354, "total_fragments": 1557, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000614145.1", "gtdb_species": "s__Bacteroides faecichinchillae", "ani": 99.9501, "matched_fragments": 1497, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.89", "min_intra_species_ani": "99.80", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_900155865.1", "gtdb_species": "s__Bacteroides bouchesdurhonensis", "ani": 94.4492, "matched_fragments": 1226, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.60", "min_intra_species_ani": "98.60", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003865075.1", "gtdb_species": "s__Bacteroides faecalis", "ani": 93.7599, "matched_fragments": 1237, "total_fragments": 1557, "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_001688725.2", "gtdb_species": "s__Bacteroides caecimuris", "ani": 81.3233, "matched_fragments": 549, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.14", "min_intra_species_ani": "95.76", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.68", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_014750685.1", "gtdb_species": "s__Bacteroides sp014750685", "ani": 80.7744, "matched_fragments": 588, "total_fragments": 1557, "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_001314995.1", "gtdb_species": "s__Bacteroides ovatus", "ani": 80.6819, "matched_fragments": 627, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.48", "min_intra_species_ani": "95.28", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.72", "num_clustered_genomes": 126, "status": "-" }, { "accession": "GCF_014334015.1", "gtdb_species": "s__Bacteroides intestinigallinarum", "ani": 80.5269, "matched_fragments": 609, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.71", "min_intra_species_ani": "95.47", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.53", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_900106755.1", "gtdb_species": "s__Bacteroides faecis", "ani": 80.3172, "matched_fragments": 658, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_000011065.1", "gtdb_species": "s__Bacteroides thetaiotaomicron", "ani": 80.0377, "matched_fragments": 608, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.45", "min_intra_species_ani": "97.24", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.75", "num_clustered_genomes": 121, "status": "-" }, { "accession": "GCA_902362375.1", "gtdb_species": "s__Bacteroides sp902362375", "ani": 79.9483, "matched_fragments": 615, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.46", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.77", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_009193295.2", "gtdb_species": "s__Bacteroides luhongzhouii", "ani": 79.8536, "matched_fragments": 582, "total_fragments": 1557, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.19", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_012113595.1", "gtdb_species": "s__Bacteroides sp012113595", "ani": 79.8223, "matched_fragments": 548, "total_fragments": 1557, "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": 0.146, "cell_length": 0.397, "doubling_h": -0.095, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 6.997, "genome_size": 4794552.5, "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 }, "_genome_taxon": [ "Bacteroides", "faecichinchillae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }