{ "type": "genome", "identifier": "GCF_000382445.1", "organism": "Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223", "title": "Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000382445.1", "bioproject": "PRJNA224116", "biosample": "SAMN02596944", "wgs_master": "AQHY00000000.1", "refseq_category": "reference genome", "taxid": "1121098", "species_taxid": "204516", "organism_name": "Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223", "infraspecific_name": "strain=DSM 17679", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/04/24", "asm_name": "Bact_mass_DSM_17679_V1", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000382445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/382/445/GCF_000382445.1_Bact_mass_DSM_17679_V1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4646209", "genome_size_ungapped": "4564584", "gc_percent": "42.500000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000382445.1-RS_2025_01_08", "annotation_date": "2025-01-08", "total_gene_count": "3949", "protein_coding_gene_count": "3762", "non_coding_gene_count": "87", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-04-24", "dateModified": "2013-04-24", "datePublished": "2013-04-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Phocaeicola massiliensis B84634 = Timone 84634 = DSM 17679 = JCM 13223" ], "sample_taxid": [ "1121098" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.295 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)": "4646209", "Number of Sequences": "15", "Longest Sequences (bp)": "3116102", "N50 (bp)": "3116102", "Gap Ratio (%)": "1.756809", "GCcontent (%)": "42.7", "Number of CDSs": "3802", "Average Protein Length": "351.7", "Coding Ratio (%)": "86.3", "Number of rRNAs": "9", "Number of tRNAs": "68", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Phocaeicola massiliensis", "strain": "strain=DSM 17679", "accession": "GCA_000382445.1", "taxid": 204516, "species_taxid": 204516, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9929, "matched_fragments": 1519, "total_fragments": 1540, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Phocaeicola massiliensis", "strain": "strain=DSM 17679", "accession": "GCA_000373085.1", "taxid": 204516, "species_taxid": 204516, "relation_to_type": "type", "validated": true, "ani": 99.9433, "matched_fragments": 1434, "total_fragments": 1540, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Phocaeicola faecalis", "strain": "strain=FXJYN30E22", "accession": "GCA_021730445.1", "taxid": 2786956, "species_taxid": 2786956, "relation_to_type": "type", "validated": true, "ani": 90.276, "matched_fragments": 1029, "total_fragments": 1540, "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": 82.6226, "matched_fragments": 644, "total_fragments": 1540, "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": 82.5007, "matched_fragments": 644, "total_fragments": 1540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola dorei", "strain": "strain=DSM 17855", "accession": "GCA_025146415.1", "taxid": 357276, "species_taxid": 357276, "relation_to_type": "type", "validated": true, "ani": 82.0923, "matched_fragments": 639, "total_fragments": 1540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola dorei", "strain": "strain=DSM 17855", "accession": "GCA_013009555.1", "taxid": 357276, "species_taxid": 357276, "relation_to_type": "type", "validated": true, "ani": 82.0052, "matched_fragments": 639, "total_fragments": 1540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola sartorii", "strain": "strain=JCM 17136", "accession": "GCA_000614185.1", "taxid": 671267, "species_taxid": 671267, "relation_to_type": "type", "validated": true, "ani": 80.8873, "matched_fragments": 564, "total_fragments": 1540, "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": 80.8691, "matched_fragments": 566, "total_fragments": 1540, "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": 79.8599, "matched_fragments": 266, "total_fragments": 1540, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Phocaeicola faecicola", "strain": "strain=AGMB03916", "accession": "GCA_013618865.1", "taxid": 2739389, "species_taxid": 2739389, "relation_to_type": "type", "validated": true, "ani": 78.9409, "matched_fragments": 221, "total_fragments": 1540, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000382445.1", "gtdb_species": "s__Phocaeicola massiliensis", "ani": 99.9929, "matched_fragments": 1517, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "98.03", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.62", "num_clustered_genomes": 25, "status": "conclusive" }, { "accession": "GCA_900760795.1", "gtdb_species": "s__Phocaeicola sp900760795", "ani": 93.8571, "matched_fragments": 776, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "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_002493165.1", "gtdb_species": "s__Phocaeicola sp002493165", "ani": 89.9725, "matched_fragments": 924, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "98.75", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000012825.1", "gtdb_species": "s__Phocaeicola vulgatus", "ani": 82.5263, "matched_fragments": 646, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.359, "mean_intra_species_ani": "98.84", "min_intra_species_ani": "95.43", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.61", "num_clustered_genomes": 263, "status": "-" }, { "accession": "GCF_013009555.1", "gtdb_species": "s__Phocaeicola dorei", "ani": 82.0123, "matched_fragments": 640, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.359, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "97.27", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.54", "num_clustered_genomes": 104, "status": "-" }, { "accession": "GCA_011959205.1", "gtdb_species": "s__Phocaeicola sp011959205", "ani": 80.9785, "matched_fragments": 509, "total_fragments": 1540, "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": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000614185.1", "gtdb_species": "s__Phocaeicola sartorii", "ani": 80.9149, "matched_fragments": 562, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "98.44", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.76", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_902388365.1", "gtdb_species": "s__Phocaeicola sp902388365", "ani": 80.2273, "matched_fragments": 557, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "97.52", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_000432735.1", "gtdb_species": "s__Phocaeicola sp000432735", "ani": 77.1717, "matched_fragments": 201, "total_fragments": 1540, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.37", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.85", "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", "massiliensis", "B84634", "=", "Timone", "84634", "=", "DSM", "17679", "=", "JCM", "13223" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }