{ "type": "genome", "identifier": "GCA_018376435.1", "organism": "Enterococcus raffinosus", "title": "Enterococcus raffinosus", "description": "derived from metagenome", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_018376435.1", "bioproject": "PRJNA698986", "biosample": "SAMN17801356", "wgs_master": "JAHABH000000000.1", "refseq_category": "na", "taxid": "71452", "species_taxid": "71452", "organism_name": "Enterococcus raffinosus", "infraspecific_name": "", "isolate": "L3_072_123G1_dasL3_072_123G1_concoct_6", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/05/16", "asm_name": "ASM1837643v1", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "GCF_018376435.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/018/376/435/GCA_018376435.1_ASM1837643v1", "excluded_from_refseq": "derived from metagenome", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-05-16", "dateModified": "2021-05-16", "datePublished": "2021-05-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus raffinosus" ], "sample_taxid": [ "71452" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Pittsburgh, Magee-Womens Hospital of UPMC" ], "sample_host_location_id": [], "data_size": "1.173 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": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "4110780", "Number of Sequences": "75", "Longest Sequences (bp)": "220136", "N50 (bp)": "124935", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.5", "Number of CDSs": "4005", "Average Protein Length": "298.2", "Coding Ratio (%)": "87.1", "Number of rRNAs": "0", "Number of tRNAs": "43", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus raffinosus", "strain": "strain=NBRC 100492", "accession": "GCA_001544115.1", "taxid": 71452, "species_taxid": 71452, "relation_to_type": "type", "validated": true, "ani": 99.523, "matched_fragments": 1204, "total_fragments": 1336, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus raffinosus", "strain": "strain=DSM 5633", "accession": "GCA_001886185.1", "taxid": 71452, "species_taxid": 71452, "relation_to_type": "type", "validated": true, "ani": 99.4793, "matched_fragments": 1214, "total_fragments": 1336, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus hulanensis", "strain": "strain=190-7", "accession": "GCA_005405485.1", "taxid": 2559929, "species_taxid": 2559929, "relation_to_type": "type", "validated": true, "ani": 82.5066, "matched_fragments": 839, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus avium", "strain": "strain=DSM 20679", "accession": "GCA_001885775.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 82.1232, "matched_fragments": 760, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus avium", "strain": "strain=ATCC 14025", "accession": "GCA_000407245.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 82.1122, "matched_fragments": 784, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus avium", "strain": "strain=NCTC9938", "accession": "GCA_900447655.1", "taxid": 33945, "species_taxid": 33945, "relation_to_type": "type", "validated": true, "ani": 82.1108, "matched_fragments": 792, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus malodoratus", "strain": "strain=DSM 20681", "accession": "GCA_001886025.1", "taxid": 71451, "species_taxid": 71451, "relation_to_type": "type", "validated": true, "ani": 81.8764, "matched_fragments": 796, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus malodoratus", "strain": "strain=NCTC12365", "accession": "GCA_900447955.1", "taxid": 71451, "species_taxid": 71451, "relation_to_type": "type", "validated": true, "ani": 81.8657, "matched_fragments": 809, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus malodoratus", "strain": "strain=ATCC 43197", "accession": "GCA_000407185.1", "taxid": 71451, "species_taxid": 71451, "relation_to_type": "type", "validated": true, "ani": 81.8335, "matched_fragments": 802, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus gilvus", "strain": "strain=ATCC BAA-350", "accession": "GCA_000394615.1", "taxid": 160453, "species_taxid": 160453, "relation_to_type": "type", "validated": true, "ani": 80.9551, "matched_fragments": 643, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus dongliensis", "strain": "strain=63-4", "accession": "GCA_005405225.1", "taxid": 2559925, "species_taxid": 2559925, "relation_to_type": "type", "validated": true, "ani": 80.8949, "matched_fragments": 362, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus alishanensis", "strain": "strain=ALS3", "accession": "GCA_019218635.1", "taxid": 1303817, "species_taxid": 1303817, "relation_to_type": "type", "validated": true, "ani": 78.0884, "matched_fragments": 186, "total_fragments": 1336, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001886185.1", "gtdb_species": "s__Enterococcus_A raffinosus", "ani": 99.498, "matched_fragments": 1213, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "97.96", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 12, "status": "conclusive" }, { "accession": "GCF_005405485.1", "gtdb_species": "s__Enterococcus_A hulanensis", "ani": 82.4891, "matched_fragments": 841, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.02", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_017315985.1", "gtdb_species": "s__Enterococcus_A sp017315985", "ani": 82.0979, "matched_fragments": 802, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "GCF_000406965.1", "gtdb_species": "s__Enterococcus_A avium", "ani": 82.0261, "matched_fragments": 790, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.01", "min_intra_species_ani": "97.91", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.78", "num_clustered_genomes": 43, "status": "-" }, { "accession": "GCF_000407185.1", "gtdb_species": "s__Enterococcus_A malodoratus", "ani": 81.8335, "matched_fragments": 802, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.27", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.84", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_018917525.1", "gtdb_species": "s__Enterococcus_A raffinosus_A", "ani": 81.5309, "matched_fragments": 764, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "GCF_005405205.1", "gtdb_species": "s__Enterococcus_A pingfangensis", "ani": 81.1611, "matched_fragments": 402, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "GCF_000407545.1", "gtdb_species": "s__Enterococcus_A gilvus", "ani": 81.003, "matched_fragments": 638, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "97.90", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.83", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_001544295.1", "gtdb_species": "s__Enterococcus_A pseudoavium", "ani": 80.9885, "matched_fragments": 496, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "GCF_005405225.1", "gtdb_species": "s__Enterococcus_A dongliensis", "ani": 80.9055, "matched_fragments": 361, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "GCF_001885905.1", "gtdb_species": "s__Enterococcus_A devriesei", "ani": 80.5965, "matched_fragments": 506, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005405345.1", "gtdb_species": "s__Enterococcus_A viikkiensis", "ani": 80.5217, "matched_fragments": 442, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "GCF_001885945.1", "gtdb_species": "s__Enterococcus_A hermanniensis", "ani": 79.8061, "matched_fragments": 405, "total_fragments": 1336, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.04, "cell_length": -0.019, "doubling_h": -0.346, "growth_tmp": 37.0, "optimum_tmp": 39.5, "optimum_ph": 9.6, "genome_size": 4116008.4, "gc_content": 39.88, "coding_genes": 2937.768, "rRNA16S_genes": 5.5, "tRNA_genes": 60.871, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 1.0, "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": 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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Enterococcaceae", "g__Enterococcus_A", "s__Enterococcus_A raffinosus" ], "_genome_taxon": [ "Enterococcus", "raffinosus", "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Enterococcaceae", "g__Enterococcus_A", "s__Enterococcus_A raffinosus", "Bacteria", "Bacillota", "Bacilli", "Lactobacillales", "Enterococcaceae", "Enterococcus", "A", "Enterococcus", "A", "raffinosus" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }