{ "type": "genome", "identifier": "GCA_902781835.1", "organism": "Erysipelothrix rhusiopathiae", "title": "Erysipelothrix rhusiopathiae", "description": "unverified source organism; derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "THE ROSLIN INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCA_902781835.1", "bioproject": "PRJEB31266", "biosample": "SAMEA6150842", "wgs_master": "CACZKR000000000.1", "refseq_category": "na", "taxid": "1648", "species_taxid": "1648", "organism_name": "Erysipelothrix rhusiopathiae", "infraspecific_name": "", "isolate": "RUG12706", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/15", "asm_name": "Rumen uncultured genome RUG12706", "submitter": "THE ROSLIN INSTITUTE", "gbrs_paired_asm": "GCF_902781835.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/781/835/GCA_902781835.1_Rumen_uncultured_genome_RUG12706", "excluded_from_refseq": "unverified source organism; derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-15", "dateModified": "2020-02-15", "datePublished": "2020-02-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Erysipelothrix rhusiopathiae" ], "sample_taxid": [ "1648" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom" ], "sample_host_location_id": [], "data_size": "0.544 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.37, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1928168", "Number of Sequences": "47", "Longest Sequences (bp)": "176449", "N50 (bp)": "59257", "Gap Ratio (%)": "0.002126", "GCcontent (%)": "38.0", "Number of CDSs": "1963", "Average Protein Length": "299.1", "Coding Ratio (%)": "91.4", "Number of rRNAs": "0", "Number of tRNAs": "47", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Absicoccus porci", "strain": "strain=YH-panp20", "accession": "GCA_003725415.1", "taxid": 2486576, "species_taxid": 2486576, "relation_to_type": "type", "validated": true, "ani": 98.3509, "matched_fragments": 560, "total_fragments": 617, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Holdemanella biformis", "strain": "strain=DSM 3989", "accession": "GCA_000156655.1", "taxid": 1735, "species_taxid": 1735, "relation_to_type": "suspected-type", "validated": true, "ani": 77.5334, "matched_fragments": 94, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Holdemanella porci", "strain": "strain=LKV-472-APC-3", "accession": "GCA_009696075.1", "taxid": 2652276, "species_taxid": 2652276, "relation_to_type": "suspected-type", "validated": true, "ani": 77.3509, "matched_fragments": 93, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Floccifex porci", "strain": "strain=LKV-178-WT-2G", "accession": "GCA_009696175.1", "taxid": 2606629, "species_taxid": 2606629, "relation_to_type": "type", "validated": true, "ani": 76.9521, "matched_fragments": 58, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Faecalicoccus acidiformans", "strain": "strain=DSM 26963", "accession": "GCA_014202635.1", "taxid": 915173, "species_taxid": 915173, "relation_to_type": "type", "validated": true, "ani": 76.8687, "matched_fragments": 53, "total_fragments": 617, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.37, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003725415.1", "gtdb_species": "s__Absicoccus porci", "ani": 98.3509, "matched_fragments": 560, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.56", "min_intra_species_ani": "98.14", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 14, "status": "conclusive" }, { "accession": "GCA_003480165.1", "gtdb_species": "s__Absicoccus sp000434355", "ani": 78.4476, "matched_fragments": 173, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "99.16", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000156655.1", "gtdb_species": "s__Holdemanella biformis", "ani": 77.5334, "matched_fragments": 94, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.82", "min_intra_species_ani": "95.86", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.56", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCA_900547815.1", "gtdb_species": "s__Holdemanella sp900547815", "ani": 77.4375, "matched_fragments": 77, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.44", "min_intra_species_ani": "96.94", "mean_intra_species_af": "0.79", "min_intra_species_af": "0.75", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_009696075.1", "gtdb_species": "s__Holdemanella porci", "ani": 77.3509, "matched_fragments": 93, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.44", "min_intra_species_ani": "95.01", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.66", "num_clustered_genomes": 21, "status": "-" }, { "accession": "GCF_000420345.1", "gtdb_species": "s__Faecalicoccus pleomorphus", "ani": 77.2097, "matched_fragments": 69, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus", "ani_circumscription_radius": 95.0413, "mean_intra_species_ani": "97.06", "min_intra_species_ani": "96.03", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.84", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCA_900754615.1", "gtdb_species": "s__Holdemanella sp900754615", "ani": 77.0512, "matched_fragments": 88, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella", "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_902399855.1", "gtdb_species": "s__Faecalicoccus sp900546545", "ani": 77.0148, "matched_fragments": 73, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus", "ani_circumscription_radius": 95.0413, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.80", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_009696175.1", "gtdb_species": "s__Floccifex porci", "ani": 76.9521, "matched_fragments": 58, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Floccifex", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.09", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014202635.1", "gtdb_species": "s__Faecalicoccus acidiformans", "ani": 76.8687, "matched_fragments": 53, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "97.66", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_900556915.1", "gtdb_species": "s__Holdemanella sp900556915", "ani": 76.6209, "matched_fragments": 55, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.25", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.83", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000469305.1", "gtdb_species": "s__Faecalitalea cylindroides", "ani": 76.5313, "matched_fragments": 59, "total_fragments": 617, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalitalea", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.51", "min_intra_species_ani": "97.31", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.75", "num_clustered_genomes": 12, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.412, "cell_length": 0.088, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 33.5, "optimum_ph": 7.4, "genome_size": 1793446.571, "gc_content": 36.465, "coding_genes": 1654.0, "rRNA16S_genes": 6.2, "tRNA_genes": 55.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_I", "c__Bacilli_A", "o__Erysipelotrichales", "f__Erysipelotrichaceae", "g__Absicoccus", "s__Absicoccus porci" ], "_genome_taxon": [ "Erysipelothrix", "rhusiopathiae", "d__Bacteria", "p__Bacillota_I", "c__Bacilli_A", "o__Erysipelotrichales", "f__Erysipelotrichaceae", "g__Absicoccus", "s__Absicoccus porci", "Bacteria", "Bacillota", "I", "Bacilli", "A", "Erysipelotrichales", "Erysipelotrichaceae", "Absicoccus", "Absicoccus", "porci" ], "_meo": [ { "id": "MEO_0000046", "label": "rumen" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }