{ "type": "genome", "identifier": "GCF_014837065.1", "organism": "Phocaeicola intestinalis", "title": "Phocaeicola intestinalis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Quadram Institutte", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014837065.1", "bioproject": "PRJNA224116", "biosample": "SAMN15803231", "wgs_master": "JACSPP000000000.1", "refseq_category": "reference genome", "taxid": "2762212", "species_taxid": "2762212", "organism_name": "Phocaeicola intestinalis", "infraspecific_name": "strain=Sa1CVN1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/30", "asm_name": "ASM1483706v1", "asm_submitter": "Quadram Institutte", "gbrs_paired_asm": "GCA_014837065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/837/065/GCF_014837065.1_ASM1483706v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4070481", "genome_size_ungapped": "4069581", "gc_percent": "45.500000", "replicon_count": "0", "scaffold_count": "162", "contig_count": "162", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014837065.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "3544", "protein_coding_gene_count": "3372", "non_coding_gene_count": "66", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-30", "dateModified": "2020-09-30", "datePublished": "2020-09-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Phocaeicola intestinalis" ], "sample_taxid": [ "2762212" ], "sample_host_organism": [ "Gallus gallus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom: Norwich" ], "sample_host_location_id": [], "data_size": "1.166 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)": "4070481", "Number of Sequences": "162", "Longest Sequences (bp)": "164077", "N50 (bp)": "54321", "Gap Ratio (%)": "0.022110", "GCcontent (%)": "45.7", "Number of CDSs": "3329", "Average Protein Length": "349.8", "Coding Ratio (%)": "85.8", "Number of rRNAs": "2", "Number of tRNAs": "60", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phocaeicola intestinalis", "strain": "strain=Sa1CVN1", "accession": "GCA_014837065.1", "taxid": 2762212, "species_taxid": 2762212, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1278, "total_fragments": 1284, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Phocaeicola salanitronis", "strain": "strain=DSM 18170", "accession": "GCA_000190575.1", "taxid": 376805, "species_taxid": 376805, "relation_to_type": "type", "validated": true, "ani": 88.5535, "matched_fragments": 705, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola barnesiae", "strain": "strain=DSM 18169", "accession": "GCA_000374585.1", "taxid": 376804, "species_taxid": 376804, "relation_to_type": "type", "validated": true, "ani": 80.2761, "matched_fragments": 294, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola barnesiae", "strain": "strain=JCM 13652", "accession": "GCA_000613645.1", "taxid": 376804, "species_taxid": 376804, "relation_to_type": "type", "validated": true, "ani": 80.1231, "matched_fragments": 288, "total_fragments": 1284, "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": 79.2445, "matched_fragments": 141, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides fluxus", "strain": "strain=YIT 12057", "accession": "GCA_000195635.1", "taxid": 626930, "species_taxid": 626930, "relation_to_type": "type", "validated": true, "ani": 79.0258, "matched_fragments": 132, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides gallinarum", "strain": "strain=DSM 18171", "accession": "GCA_000374365.1", "taxid": 376806, "species_taxid": 376806, "relation_to_type": "type", "validated": true, "ani": 78.9728, "matched_fragments": 147, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola faecium", "strain": "strain=Sa1YUN3", "accession": "GCA_014837055.1", "taxid": 2762213, "species_taxid": 2762213, "relation_to_type": "type", "validated": true, "ani": 78.8992, "matched_fragments": 264, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola coprocola", "strain": "strain=DSM 17136", "accession": "GCA_000154845.1", "taxid": 310298, "species_taxid": 310298, "relation_to_type": "suspected-type", "validated": true, "ani": 78.767, "matched_fragments": 274, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola plebeius", "strain": "strain=DSM 17135", "accession": "GCA_000187895.1", "taxid": 310297, "species_taxid": 310297, "relation_to_type": "suspected-type", "validated": true, "ani": 78.5738, "matched_fragments": 259, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola coprophilus", "strain": "strain=DSM 18228", "accession": "GCA_000157915.1", "taxid": 387090, "species_taxid": 387090, "relation_to_type": "type", "validated": true, "ani": 78.3385, "matched_fragments": 215, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola coprophilus", "strain": "strain=JCM 13818", "accession": "GCA_001315785.1", "taxid": 387090, "species_taxid": 387090, "relation_to_type": "type", "validated": true, "ani": 78.3288, "matched_fragments": 209, "total_fragments": 1284, "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": 77.8726, "matched_fragments": 161, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola vulgatus", "strain": "strain=FDAARGOS_1098", "accession": "GCA_016766915.1", "taxid": 821, "species_taxid": 821, "relation_to_type": "type", "validated": true, "ani": 77.4219, "matched_fragments": 159, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola vulgatus", "strain": "strain=ATCC 8482", "accession": "GCA_000012825.1", "taxid": 821, "species_taxid": 821, "relation_to_type": "type", "validated": true, "ani": 77.4103, "matched_fragments": 155, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bacteroides fragilis", "strain": "strain=ATCC 25285", "accession": "GCA_001997325.1", "taxid": 817, "species_taxid": 817, "relation_to_type": "type", "validated": true, "ani": 77.1916, "matched_fragments": 94, "total_fragments": 1284, "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": 77.1902, "matched_fragments": 102, "total_fragments": 1284, "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": 77.1597, "matched_fragments": 99, "total_fragments": 1284, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016899805.1", "gtdb_species": "s__Phocaeicola gallinaceus", "ani": 98.2011, "matched_fragments": 1003, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.20", "min_intra_species_ani": "97.80", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.74", "num_clustered_genomes": 12, "status": "conclusive" }, { "accession": "GCF_000190575.1", "gtdb_species": "s__Phocaeicola salanitronis", "ani": 88.5721, "matched_fragments": 704, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "97.68", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900546355.1", "gtdb_species": "s__Phocaeicola sp900546355", "ani": 85.5251, "matched_fragments": 589, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002161765.1", "gtdb_species": "s__Phocaeicola merdavium", "ani": 81.9375, "matched_fragments": 598, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.33", "min_intra_species_ani": "98.22", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_900544675.1", "gtdb_species": "s__Phocaeicola sp900544675", "ani": 81.2892, "matched_fragments": 655, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_016901995.1", "gtdb_species": "s__Phocaeicola sp900066445", "ani": 80.8055, "matched_fragments": 169, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.12", "min_intra_species_ani": "97.12", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.79", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000374585.1", "gtdb_species": "s__Phocaeicola barnesiae", "ani": 80.2633, "matched_fragments": 294, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.58", "min_intra_species_ani": "98.10", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_016900355.1", "gtdb_species": "s__Phocaeicola sp900551065", "ani": 78.9271, "matched_fragments": 264, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.34", "min_intra_species_ani": "95.04", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.84", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000154845.1", "gtdb_species": "s__Phocaeicola coprocola", "ani": 78.7115, "matched_fragments": 276, "total_fragments": 1284, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.02", "min_intra_species_ani": "97.39", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.65", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCA_019116045.1", "gtdb_species": "s__Bacteroides merdipullorum", "ani": 77.5853, "matched_fragments": 116, "total_fragments": 1284, "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_000436795.1", "gtdb_species": "s__Phocaeicola sp000436795", "ani": 77.4308, "matched_fragments": 204, "total_fragments": 1284, "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": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.523, "cell_length": -0.523, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": null, "genome_size": 2530631.0, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Phocaeicola", "intestinalis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }