{ "type": "genome", "identifier": "GCF_000169255.2", "organism": "Pseudoflavonifractor capillosus ATCC 29799", "title": "Pseudoflavonifractor capillosus ATCC 29799", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Washington University Genome Sequencing Center", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000169255.2", "bioproject": "PRJNA224116", "biosample": "SAMN00627059", "wgs_master": "AAXG00000000.2", "refseq_category": "reference genome", "taxid": "411467", "species_taxid": "106588", "organism_name": "Pseudoflavonifractor capillosus ATCC 29799", "infraspecific_name": "strain=ATCC 29799", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/02/09", "asm_name": "ASM16925v2", "asm_submitter": "Washington University Genome Sequencing Center", "gbrs_paired_asm": "GCA_000169255.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/169/255/GCF_000169255.2_ASM16925v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4241076", "genome_size_ungapped": "4241076", "gc_percent": "59.000000", "replicon_count": "0", "scaffold_count": "65", "contig_count": "65", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000169255.2-RS_2024_04_11", "annotation_date": "2024-04-11", "total_gene_count": "4067", "protein_coding_gene_count": "3900", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-02-09", "dateModified": "2009-02-09", "datePublished": "2009-02-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoflavonifractor capillosus ATCC 29799" ], "sample_taxid": [ "411467" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not determined" ], "sample_host_location_id": [], "data_size": "1.187 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4241076", "Number of Sequences": "65", "Longest Sequences (bp)": "360228", "N50 (bp)": "157028", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.1", "Number of CDSs": "3955", "Average Protein Length": "315.1", "Coding Ratio (%)": "88.2", "Number of rRNAs": "4", "Number of tRNAs": "58", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoflavonifractor gallinarum", "strain": "strain=DSM 107456", "accession": "GCA_014982855.1", "taxid": 2779352, "species_taxid": 2779352, "relation_to_type": "type", "validated": true, "ani": 82.2096, "matched_fragments": 449, "total_fragments": 1377, "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": 81.7122, "matched_fragments": 515, "total_fragments": 1377, "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": 81.5985, "matched_fragments": 486, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dysosmobacter welbionis", "strain": "strain=J115", "accession": "GCA_005121165.3", "taxid": 2093857, "species_taxid": 2093857, "relation_to_type": "type", "validated": true, "ani": 80.5064, "matched_fragments": 274, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalibacterium duncaniae", "strain": "strain=A2-165", "accession": "GCA_000162015.1", "taxid": 411483, "species_taxid": 411483, "relation_to_type": "type", "validated": true, "ani": 80.4041, "matched_fragments": 151, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalibacterium duncaniae", "strain": "strain=JCM 31915", "accession": "GCA_010509575.1", "taxid": 411483, "species_taxid": 411483, "relation_to_type": "type", "validated": true, "ani": 80.1156, "matched_fragments": 152, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Clostridium phoceensis", "strain": "strain=GD3", "accession": "GCA_001244495.1", "taxid": 1650661, "species_taxid": 1650661, "relation_to_type": "type", "validated": true, "ani": 79.8284, "matched_fragments": 354, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Intestinimonas butyriciproducens", "strain": "strain=SRB-521-5-I", "accession": "GCA_004154955.1", "taxid": 1297617, "species_taxid": 1297617, "relation_to_type": "type", "validated": true, "ani": 79.1568, "matched_fragments": 338, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Intestinimonas butyriciproducens", "strain": "strain=DSM 26588", "accession": "GCA_024622565.1", "taxid": 1297617, "species_taxid": 1297617, "relation_to_type": "type", "validated": true, "ani": 79.1084, "matched_fragments": 324, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Intestinimonas butyriciproducens", "strain": "strain=DSM 26588", "accession": "GCA_003096335.1", "taxid": 1297617, "species_taxid": 1297617, "relation_to_type": "type", "validated": true, "ani": 79.0773, "matched_fragments": 343, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Dysosmobacter acutus", "strain": "strain=MSJ-2", "accession": "GCA_018919205.1", "taxid": 2841504, "species_taxid": 2841504, "relation_to_type": "type", "validated": true, "ani": 78.4426, "matched_fragments": 195, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Papillibacter cinnamivorans", "strain": "strain=DSM 12816", "accession": "GCA_900176335.1", "taxid": 100176, "species_taxid": 100176, "relation_to_type": "type", "validated": true, "ani": 76.7117, "matched_fragments": 100, "total_fragments": 1377, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 2.78, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000169255.2", "gtdb_species": "s__Pseudoflavonifractor capillosus", "ani": 100.0, "matched_fragments": 1376, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.82", "min_intra_species_ani": "95.81", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_904419835.1", "gtdb_species": "s__Pseudoflavonifractor sp904419835", "ani": 91.4924, "matched_fragments": 684, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor", "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_002161215.1", "gtdb_species": "s__Flavonifractor avistercoris", "ani": 82.9905, "matched_fragments": 562, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.82", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002159265.1", "gtdb_species": "s__Flavonifractor sp002159265", "ani": 82.9428, "matched_fragments": 518, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor", "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_002160305.1", "gtdb_species": "s__Lawsonibacter pullicola", "ani": 82.5816, "matched_fragments": 420, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.75", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_900626145.1", "gtdb_species": "s__Intestinimonas timonensis", "ani": 82.4342, "matched_fragments": 462, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas", "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_017811815.1", "gtdb_species": "s__Flavonifractor sp017811815", "ani": 81.9871, "matched_fragments": 497, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor", "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_002161085.1", "gtdb_species": "s__Flavonifractor avicola", "ani": 81.7981, "matched_fragments": 461, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.94", "min_intra_species_ani": "96.68", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.78", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_019119165.1", "gtdb_species": "s__Flavonifractor intestinigallinarum", "ani": 81.6049, "matched_fragments": 377, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.85", "min_intra_species_ani": "97.85", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018711785.1", "gtdb_species": "s__Galloscillospira_A excrementavium", "ani": 81.5728, "matched_fragments": 319, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "98.56", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014287675.1", "gtdb_species": "s__Pseudoflavonifractor sp014287675", "ani": 81.4648, "matched_fragments": 589, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.22", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCA_018715695.1", "gtdb_species": "s__Galloscillospira_A stercoripullorum", "ani": 81.1996, "matched_fragments": 328, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "99.04", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900549565.1", "gtdb_species": "s__UMGS1202 sp900549565", "ani": 81.198, "matched_fragments": 453, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202", "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_014287895.1", "gtdb_species": "s__NSJ-51 sp900549795", "ani": 80.6744, "matched_fragments": 422, "total_fragments": 1377, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "99.06", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": 0.204, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 4241464.5, "gc_content": 59.115, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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": [ "Pseudoflavonifractor", "capillosus", "ATCC", "29799" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }