{ "type": "genome", "identifier": "GCF_005405205.1", "organism": "Enterococcus pingfangensis", "title": "Enterococcus pingfangensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Northeast Agricultural University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_005405205.1", "bioproject": "PRJNA224116", "biosample": "SAMD00164306", "wgs_master": "BJDP00000000.1", "refseq_category": "reference genome", "taxid": "2559924", "species_taxid": "2559924", "organism_name": "Enterococcus pingfangensis", "infraspecific_name": "strain=241-2-2", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/29", "asm_name": "ASM540520v1", "asm_submitter": "Northeast Agricultural University", "gbrs_paired_asm": "GCA_005405205.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/005/405/205/GCF_005405205.1_ASM540520v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2017363", "genome_size_ungapped": "2017363", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "24", "contig_count": "24", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_005405205.1-RS_2024_08_26", "annotation_date": "2024-08-26", "total_gene_count": "1960", "protein_coding_gene_count": "1873", "non_coding_gene_count": "59", "pubmed_id": "31339483" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-29", "dateModified": "2019-03-29", "datePublished": "2019-03-29", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterococcus pingfangensis" ], "sample_taxid": [ "2559924" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "0.572 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)": "2017363", "Number of Sequences": "24", "Longest Sequences (bp)": "350362", "N50 (bp)": "203181", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.1", "Number of CDSs": "1917", "Average Protein Length": "304.5", "Coding Ratio (%)": "86.8", "Number of rRNAs": "2", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterococcus pingfangensis", "strain": "strain=241-2-2", "accession": "GCA_005405205.1", "taxid": 2559924, "species_taxid": 2559924, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 661, "total_fragments": 661, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterococcus xiangfangensis", "strain": "strain=11097", "accession": "GCA_005405365.1", "taxid": 1296537, "species_taxid": 1296537, "relation_to_type": "type", "validated": true, "ani": 92.0599, "matched_fragments": 571, "total_fragments": 661, "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": 83.5656, "matched_fragments": 397, "total_fragments": 661, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus hulanensis", "strain": "strain=190-7", "accession": "GCA_005405485.1", "taxid": 2559929, "species_taxid": 2559929, "relation_to_type": "type", "validated": true, "ani": 81.7531, "matched_fragments": 445, "total_fragments": 661, "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": 81.5675, "matched_fragments": 457, "total_fragments": 661, "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": 81.5469, "matched_fragments": 445, "total_fragments": 661, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterococcus pseudoavium", "strain": "strain=NBRC 100491", "accession": "GCA_001544295.1", "taxid": 44007, "species_taxid": 44007, "relation_to_type": "type", "validated": true, "ani": 81.2588, "matched_fragments": 392, "total_fragments": 661, "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": 80.9769, "matched_fragments": 414, "total_fragments": 661, "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": 78.2053, "matched_fragments": 167, "total_fragments": 661, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_005405205.1", "gtdb_species": "s__Enterococcus_A pingfangensis", "ani": 100.0, "matched_fragments": 661, "total_fragments": 661, "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": "conclusive" }, { "accession": "GCF_005405365.1", "gtdb_species": "s__Enterococcus_A xiangfangensis", "ani": 92.0599, "matched_fragments": 571, "total_fragments": 661, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.65", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005405225.1", "gtdb_species": "s__Enterococcus_A dongliensis", "ani": 83.6063, "matched_fragments": 395, "total_fragments": 661, "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_005405485.1", "gtdb_species": "s__Enterococcus_A hulanensis", "ani": 81.7641, "matched_fragments": 444, "total_fragments": 661, "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_000407185.1", "gtdb_species": "s__Enterococcus_A malodoratus", "ani": 81.5518, "matched_fragments": 458, "total_fragments": 661, "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": 81.4429, "matched_fragments": 412, "total_fragments": 661, "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_001544295.1", "gtdb_species": "s__Enterococcus_A pseudoavium", "ani": 81.2588, "matched_fragments": 392, "total_fragments": 661, "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": 81.0899, "matched_fragments": 424, "total_fragments": 661, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.04, "cell_length": -0.019, "doubling_h": -0.346, "growth_tmp": 36.238, "optimum_tmp": 34.173, "optimum_ph": 8.805, "genome_size": 3255020.058, "gc_content": 38.565, "coding_genes": 2937.768, "rRNA16S_genes": 5.5, "tRNA_genes": 60.871, "gram_stain": 1.0, "sporulation": 0.062, "motility": 0.0, "range_salinity": 1.0, "facultative_respiration": 0.229, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.77, 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