{ "type": "genome", "identifier": "GCF_000407225.1", "organism": "Enterococcus columbae DSM 7374 = ATCC 51263", "title": "Enterococcus columbae DSM 7374 = ATCC 51263", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000407225.1", "bioproject": "PRJNA224116", "biosample": "SAMN02596961", "wgs_master": "ASWJ00000000.1", "refseq_category": "reference genome", "taxid": "1121865", "species_taxid": "1355", "organism_name": "Enterococcus columbae DSM 7374 = ATCC 51263", "infraspecific_name": "strain=ATCC 51263", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/06/04", "asm_name": "Ente_colu_ATCC51263_V2", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000407225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/407/225/GCF_000407225.1_Ente_colu_ATCC51263_V2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2545099", "genome_size_ungapped": "2542704", "gc_percent": "36.500000", "replicon_count": "0", "scaffold_count": "9", "contig_count": "12", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000407225.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "2380", "protein_coding_gene_count": "2289", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-06-04", "dateModified": "2013-06-04", "datePublished": "2013-06-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus columbae DSM 7374 = ATCC 51263" ], "sample_taxid": [ "1121865" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.713 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)": "2545099", "Number of Sequences": "9", "Longest Sequences (bp)": "630642", "N50 (bp)": "421089", "Gap Ratio (%)": "0.094102", "GCcontent (%)": "36.3", "Number of CDSs": "2350", "Average Protein Length": "309.9", "Coding Ratio (%)": "85.8", "Number of rRNAs": "6", "Number of tRNAs": "37", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus columbae", "strain": "strain=ATCC 51263", "accession": "GCA_000407225.1", "taxid": 1355, "species_taxid": 1355, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 844, "total_fragments": 844, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus columbae", "strain": "strain=ATCC 51263", "accession": "GCA_000406925.1", "taxid": 1355, "species_taxid": 1355, "relation_to_type": "type", "validated": true, "ani": 99.9659, "matched_fragments": 840, "total_fragments": 844, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus columbae", "strain": "strain=DSM 7374", "accession": "GCA_000373065.1", "taxid": 1355, "species_taxid": 1355, "relation_to_type": "type", "validated": true, "ani": 99.9559, "matched_fragments": 808, "total_fragments": 844, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus columbae", "strain": "strain=DSM 7374", "accession": "GCA_001885835.1", "taxid": 1355, "species_taxid": 1355, "relation_to_type": "type", "validated": true, "ani": 99.9053, "matched_fragments": 792, "total_fragments": 844, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus cecorum", "strain": "strain=ATCC 43198", "accession": "GCA_000492155.1", "taxid": 44008, "species_taxid": 44008, "relation_to_type": "type", "validated": true, "ani": 80.2802, "matched_fragments": 328, "total_fragments": 844, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus saccharolyticus subsp. saccharolyticus", "strain": "strain=ATCC 43076", "accession": "GCA_000407005.1", "taxid": 1814218, "species_taxid": 41997, "relation_to_type": "type", "validated": true, "ani": 78.7827, "matched_fragments": 157, "total_fragments": 844, "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": 78.0447, "matched_fragments": 77, "total_fragments": 844, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus humatus", "strain": "strain=JCM 31581", "accession": "GCA_003950325.1", "taxid": 1889241, "species_taxid": 1889241, "relation_to_type": "type", "validated": true, "ani": 77.7619, "matched_fragments": 69, "total_fragments": 844, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus alcedinis", "strain": "strain=CCM 8433", "accession": "GCA_014635985.1", "taxid": 1274384, "species_taxid": 1274384, "relation_to_type": "type", "validated": true, "ani": 77.6427, "matched_fragments": 100, "total_fragments": 844, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Vagococcus allomyrinae", "strain": "strain=BWB3-3", "accession": "GCA_017829975.1", "taxid": 2794353, "species_taxid": 2794353, "relation_to_type": "type", "validated": true, "ani": 77.2417, "matched_fragments": 63, "total_fragments": 844, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000406925.1", "gtdb_species": "s__Enterococcus_E columbae", "ani": 99.9659, "matched_fragments": 839, "total_fragments": 844, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 4, "status": "conclusive" }, { "accession": "GCF_000407565.1", "gtdb_species": "s__Enterococcus_E cecorum", "ani": 80.3453, "matched_fragments": 339, "total_fragments": 844, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.77", "min_intra_species_ani": "96.06", "mean_intra_species_af": "0.87", 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"num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000407285.1", "gtdb_species": "s__Enterococcus_F saccharolyticus", "ani": 78.5143, "matched_fragments": 149, "total_fragments": 844, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_F", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001465345.1", "gtdb_species": "s__Enterococcus rotai", "ani": 78.4046, "matched_fragments": 85, "total_fragments": 844, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus", "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": 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