{ "type": "genome", "identifier": "GCF_000340375.1", "organism": "Eggerthia catenaformis OT 569 = DSM 20559", "title": "Eggerthia catenaformis OT 569 = DSM 20559", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000340375.1", "bioproject": "PRJNA224116", "biosample": "SAMN02596729", "wgs_master": "AGEJ00000000.1", "refseq_category": "reference genome", "taxid": "999415", "species_taxid": "31973", "organism_name": "Eggerthia catenaformis OT 569 = DSM 20559", "infraspecific_name": "strain=OT 569", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/02/19", "asm_name": "Lact_cate_OT_569_V1", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000340375.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/340/375/GCF_000340375.1_Lact_cate_OT_569_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": "1945158", "genome_size_ungapped": "1935589", "gc_percent": "33.000000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "36", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000340375.1-RS_2024_04_21", "annotation_date": "2024-04-21", "total_gene_count": "1956", "protein_coding_gene_count": "1847", "non_coding_gene_count": "74", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-02-19", "dateModified": "2013-02-19", "datePublished": "2013-02-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Eggerthia catenaformis OT 569 = DSM 20559" ], "sample_taxid": [ "999415" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.534 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)": "1945158", "Number of Sequences": "8", "Longest Sequences (bp)": "506876", "N50 (bp)": "477408", "Gap Ratio (%)": "0.491939", "GCcontent (%)": "32.8", "Number of CDSs": "1881", "Average Protein Length": "298.5", "Coding Ratio (%)": "86.6", "Number of rRNAs": "12", "Number of tRNAs": "47", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Eggerthia catenaformis", "strain": "strain=OT 569", "accession": "GCA_000340375.1", "taxid": 31973, "species_taxid": 31973, "relation_to_type": "type", "validated": true, "ani": 99.9999, "matched_fragments": 636, "total_fragments": 644, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Eggerthia catenaformis", "strain": "strain=DSM 20559", "accession": "GCA_000422605.1", "taxid": 31973, "species_taxid": 31973, "relation_to_type": "type", "validated": true, "ani": 98.7766, "matched_fragments": 554, "total_fragments": 644, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Catenibacterium mitsuokai", "strain": "strain=DSM 15897", "accession": "GCA_025148785.1", "taxid": 100886, "species_taxid": 100886, "relation_to_type": "suspected-type", "validated": true, "ani": 78.1684, "matched_fragments": 111, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Coprobacillus cateniformis", "strain": "strain=RCA1-24", "accession": "GCA_009767585.1", "taxid": 100884, "species_taxid": 100884, "relation_to_type": "type", "validated": true, "ani": 77.9119, "matched_fragments": 85, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Tannockella kyphosi", "strain": "strain=BP52G", "accession": "GCA_021054785.1", "taxid": 2899121, "species_taxid": 2899121, "relation_to_type": "type", "validated": true, "ani": 77.9026, "matched_fragments": 57, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sharpea porci", "strain": "strain=CA-Schmier-601-WT-3", "accession": "GCA_009695655.1", "taxid": 2652286, "species_taxid": 2652286, "relation_to_type": "type", "validated": true, "ani": 77.6609, "matched_fragments": 112, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kandleria vitulina", "strain": "strain=DSM 20405", "accession": "GCA_001436965.1", "taxid": 1630, "species_taxid": 1630, "relation_to_type": "type", "validated": true, "ani": 77.0068, "matched_fragments": 106, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalibacillus intestinalis", "strain": "strain=SNUG30099", "accession": "GCA_003024685.1", "taxid": 1982626, "species_taxid": 1982626, "relation_to_type": "type", "validated": true, "ani": 76.5231, "matched_fragments": 78, "total_fragments": 644, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000340375.1", "gtdb_species": "s__Eggerthia catenaformis", "ani": 99.9999, "matched_fragments": 637, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Eggerthia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.71", "min_intra_species_ani": "98.60", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_009767585.1", "gtdb_species": "s__Coprobacillus cateniformis", "ani": 77.8045, "matched_fragments": 83, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Coprobacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.28", "min_intra_species_ani": "99.05", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_000702165.1", "gtdb_species": "s__Sharpea azabuensis", "ani": 77.5323, "matched_fragments": 97, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Sharpea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.40", "min_intra_species_ani": "97.32", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.79", "num_clustered_genomes": 46, "status": "-" }, { "accession": "GCF_000702065.1", "gtdb_species": "s__Kandleria vitulina", "ani": 77.0778, "matched_fragments": 107, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Kandleria", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.86", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_004168205.1", "gtdb_species": "s__Catenibacterium sp000437715", "ani": 77.0223, "matched_fragments": 88, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.65", "min_intra_species_ani": "95.64", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.75", "num_clustered_genomes": 29, "status": "-" }, { "accession": "GCF_000173795.1", "gtdb_species": "s__Catenibacterium mitsuokai", "ani": 76.9497, "matched_fragments": 95, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.03", "min_intra_species_ani": "96.27", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.73", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCA_910588075.1", "gtdb_species": "s__MGBC163490 sp910588075", "ani": 76.9261, "matched_fragments": 89, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490", "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_900540685.1", "gtdb_species": "s__Catenibacterium sp900540685", "ani": 76.7614, "matched_fragments": 87, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium", "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": "GCA_900540665.1", "gtdb_species": "s__Catenibacterium sp900540665", "ani": 76.6342, "matched_fragments": 84, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "99.03", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000455285.1", "gtdb_species": "s__Stoquefichus massiliensis", "ani": 76.5562, "matched_fragments": 113, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003024685.1", "gtdb_species": "s__Faecalibacillus intestinalis", "ani": 76.5231, "matched_fragments": 78, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "96.13", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.76", "num_clustered_genomes": 51, "status": "-" }, { "accession": "GCF_016901755.1", "gtdb_species": "s__Faecalibacillus spiroforme_A", "ani": 76.222, "matched_fragments": 60, "total_fragments": 644, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "98.79", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 41.0, "optimum_ph": null, "genome_size": 1935589.0, "gc_content": 32.8, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "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": [ "Eggerthia", "catenaformis", "OT", "569", "=", "DSM", "20559" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }