{ "type": "genome", "identifier": "GCF_025144995.1", "organism": "Alistipes indistinctus YIT 12060", "title": "Alistipes indistinctus YIT 12060", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Stanford University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025144995.1", "bioproject": "PRJNA224116", "biosample": "SAMN20222634", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "742725", "species_taxid": "626932", "organism_name": "Alistipes indistinctus YIT 12060", "infraspecific_name": "strain=YIT 12060", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/09/12", "asm_name": "ASM2514499v1", "asm_submitter": "Stanford University", "gbrs_paired_asm": "GCA_025144995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/144/995/GCF_025144995.1_ASM2514499v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2857445", "genome_size_ungapped": "2857445", "gc_percent": "55.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025144995.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "2367", "protein_coding_gene_count": "2293", "non_coding_gene_count": "53", "pubmed_id": "36070752" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-09-12", "dateModified": "2022-09-12", "datePublished": "2022-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Alistipes indistinctus YIT 12060" ], "sample_taxid": [ "742725" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "0.808 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)": "2857445", "Number of Sequences": "1", "Longest Sequences (bp)": "2857445", "N50 (bp)": "2857445", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.8", "Number of CDSs": "2331", "Average Protein Length": "355.3", "Coding Ratio (%)": "86.9", "Number of rRNAs": "6", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Alistipes indistinctus", "strain": "strain=YIT 12060", "accession": "GCA_025144995.1", "taxid": 626932, "species_taxid": 626932, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 951, "total_fragments": 952, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Alistipes indistinctus", "strain": "strain=YIT 12060", "accession": "GCA_000231275.1", "taxid": 626932, "species_taxid": 626932, "relation_to_type": "type", "validated": true, "ani": 99.9824, "matched_fragments": 948, "total_fragments": 952, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Alistipes ihumii", "strain": "strain=AP11", "accession": "GCA_025144665.1", "taxid": 1470347, "species_taxid": 1470347, "relation_to_type": "type", "validated": true, "ani": 78.2182, "matched_fragments": 238, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes ihumii", "strain": "strain=AP11", "accession": "GCA_000321205.1", "taxid": 1470347, "species_taxid": 1470347, "relation_to_type": "type", "validated": true, "ani": 77.9893, "matched_fragments": 234, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes onderdonkii subsp. vulgaris", "strain": "strain=3BBH6", "accession": "GCA_006542645.1", "taxid": 2585117, "species_taxid": 328813, "relation_to_type": "type", "validated": true, "ani": 77.5888, "matched_fragments": 122, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gallalistipes aquisgranensis", "strain": "strain=DSM 108975", "accession": "GCA_014982715.1", "taxid": 2779358, "species_taxid": 2779358, "relation_to_type": "type", "validated": true, "ani": 77.4041, "matched_fragments": 157, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes onderdonkii", "strain": "strain=DSM 19147", "accession": "GCA_025145285.1", "taxid": 328813, "species_taxid": 328813, "relation_to_type": "type", "validated": true, "ani": 77.3503, "matched_fragments": 121, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes montrealensis", "strain": "strain=kh20", "accession": "GCA_018362775.1", "taxid": 2834113, "species_taxid": 2834113, "relation_to_type": "type", "validated": true, "ani": 77.1931, "matched_fragments": 115, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes onderdonkii", "strain": "strain=DSM 19147", "accession": "GCA_000374505.1", "taxid": 328813, "species_taxid": 328813, "relation_to_type": "type", "validated": true, "ani": 77.183, "matched_fragments": 117, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Alistipes shahii", "strain": "strain=WAL 8301", "accession": "GCA_000210575.1", "taxid": 328814, "species_taxid": 328814, "relation_to_type": "suspected-type", "validated": true, "ani": 77.1646, "matched_fragments": 120, "total_fragments": 952, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000231275.1", "gtdb_species": "s__Alistipes_A indistinctus", "ani": 99.9824, "matched_fragments": 948, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "99.01", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_009557455.1", "gtdb_species": "s__Alistipes_A pullistercoris", "ani": 78.3467, "matched_fragments": 233, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "98.63", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCA_900545315.1", "gtdb_species": "s__Alistipes_A sp900545315", "ani": 78.1582, "matched_fragments": 274, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000321205.1", "gtdb_species": "s__Alistipes_A ihumii", "ani": 77.9893, "matched_fragments": 234, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "98.23", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_900539755.1", "gtdb_species": "s__Alistipes_A sp900539755", "ani": 77.9561, "matched_fragments": 240, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "96.99", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_017415005.1", "gtdb_species": "s__RGIG1874 sp017415005", "ani": 77.9066, "matched_fragments": 172, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG1874", "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_910583985.1", "gtdb_species": "s__Alistipes_A sp910583985", "ani": 77.76, "matched_fragments": 212, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "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_900549685.1", "gtdb_species": "s__Alistipes_A sp900549685", "ani": 77.6296, "matched_fragments": 183, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A", "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_014982715.1", "gtdb_species": "s__DSM-108975 sp014982715", "ani": 77.4041, "matched_fragments": 157, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975", "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_900290115.1", "gtdb_species": "s__Alistipes excrementigallinarum", "ani": 77.1902, "matched_fragments": 93, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_017935625.1", "gtdb_species": "s__RGIG9113 sp017935625", "ani": 77.0453, "matched_fragments": 86, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113", "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_019116245.1", "gtdb_species": "s__Tidjanibacter faecipullorum", "ani": 76.6811, "matched_fragments": 89, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter", "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_905214725.1", "gtdb_species": "s__Alistipes sp905214725", "ani": 76.5579, "matched_fragments": 72, "total_fragments": 952, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes", "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": -0.26, "cell_length": 0.23, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.0, "genome_size": 2850978.0, "gc_content": 56.414, "coding_genes": 2833.0, "rRNA16S_genes": 2.0, "tRNA_genes": 48.0, "gram_stain": 0.0, "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": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Alistipes", "indistinctus", "YIT", "12060" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }