{ "type": "genome", "identifier": "GCF_016481285.1", "organism": "Streptococcus zalophi", "title": "Streptococcus zalophi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US FDA", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016481285.1", "bioproject": "PRJNA224116", "biosample": "SAMN17185282", "wgs_master": "JAENBP000000000.1", "refseq_category": "reference genome", "taxid": "640031", "species_taxid": "640031", "organism_name": "Streptococcus zalophi", "infraspecific_name": "strain=CSL7508", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/01/04", "asm_name": "ASM1648128v1", "asm_submitter": "US FDA", "gbrs_paired_asm": "GCA_016481285.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/481/285/GCF_016481285.1_ASM1648128v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1581094", "genome_size_ungapped": "1581094", "gc_percent": "35.000000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016481285.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "1499", "protein_coding_gene_count": "1438", "non_coding_gene_count": "48", "pubmed_id": "33999792" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-01-04", "dateModified": "2021-01-04", "datePublished": "2021-01-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptococcus zalophi" ], "sample_taxid": [ "640031" ], "sample_host_organism": [ "Zalophus californianus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: The Marine Mammal Center, California" ], "sample_host_location_id": [], "data_size": "0.442 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)": "1581094", "Number of Sequences": "20", "Longest Sequences (bp)": "338197", "N50 (bp)": "222165", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "34.8", "Number of CDSs": "1431", "Average Protein Length": "320.9", "Coding Ratio (%)": "87.1", "Number of rRNAs": "3", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptococcus zalophi", "strain": "strain=CSL7508", "accession": "GCA_016481285.1", "taxid": 640031, "species_taxid": 640031, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 518, "total_fragments": 518, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptococcus pacificus", "strain": "strain=CSL7591", "accession": "GCA_016481305.1", "taxid": 2740577, "species_taxid": 2740577, "relation_to_type": "type", "validated": true, "ani": 87.9121, "matched_fragments": 447, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus marimammalium", "strain": "strain=DSM 18627", "accession": "GCA_000380045.1", "taxid": 269666, "species_taxid": 269666, "relation_to_type": "type", "validated": true, "ani": 87.4657, "matched_fragments": 409, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus hyointestinalis", "strain": "strain=NCTC12224", "accession": "GCA_900459405.1", "taxid": 1337, "species_taxid": 1337, "relation_to_type": "type", "validated": true, "ani": 78.5572, "matched_fragments": 59, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus agalactiae", "strain": "strain=NCTC8181", "accession": "GCA_900458965.1", "taxid": 1311, "species_taxid": 1311, "relation_to_type": "suspected-type", "validated": true, "ani": 78.5024, "matched_fragments": 85, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus agalactiae", "strain": "strain=ATCC 13813", "accession": "GCA_000186445.1", "taxid": 1311, "species_taxid": 1311, "relation_to_type": "type", "validated": true, "ani": 78.4549, "matched_fragments": 87, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus downii", "strain": "strain=CECT 9732", "accession": "GCA_004353325.1", "taxid": 1968889, "species_taxid": 1968889, "relation_to_type": "type", "validated": true, "ani": 78.3545, "matched_fragments": 59, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus catagoni", "strain": "strain=99-1/2017", "accession": "GCA_011421425.1", "taxid": 2654874, "species_taxid": 2654874, "relation_to_type": "type", "validated": true, "ani": 78.3299, "matched_fragments": 85, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus porcinus", "strain": "strain=NCTC10999", "accession": "GCA_900475415.1", "taxid": 1340, "species_taxid": 1340, "relation_to_type": "type", "validated": true, "ani": 78.2908, "matched_fragments": 88, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus vicugnae", "strain": "strain=SL1232", "accession": "GCA_016461705.1", "taxid": 2740579, "species_taxid": 2740579, "relation_to_type": "type", "validated": true, "ani": 78.182, "matched_fragments": 102, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus dysgalactiae", "strain": "strain=FDAARGOS_1157", "accession": "GCA_016724885.1", "taxid": 1334, "species_taxid": 1334, "relation_to_type": "type", "validated": true, "ani": 78.0368, "matched_fragments": 87, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus urinalis", "strain": "strain=NCTC13766", "accession": "GCA_900636885.1", "taxid": 149016, "species_taxid": 149016, "relation_to_type": "type", "validated": true, "ani": 78.0206, "matched_fragments": 105, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus urinalis", "strain": "strain=2285-97", "accession": "GCA_000188055.3", "taxid": 149016, "species_taxid": 149016, "relation_to_type": "type", "validated": true, "ani": 77.9774, "matched_fragments": 106, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus thoraltensis", "strain": "strain=DSM 12221", "accession": "GCA_000380145.1", "taxid": 55085, "species_taxid": 55085, "relation_to_type": "type", "validated": true, "ani": 77.826, "matched_fragments": 88, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus shenyangsis", "strain": "strain=D19", "accession": "GCA_006385785.1", "taxid": 2589786, "species_taxid": 2589786, "relation_to_type": "type", "validated": true, "ani": 77.767, "matched_fragments": 66, "total_fragments": 518, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016481285.1", "gtdb_species": "s__Streptococcus zalophi", "ani": 100.0, "matched_fragments": 518, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "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_016481305.1", "gtdb_species": "s__Streptococcus pacificus", "ani": 87.9121, "matched_fragments": 447, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "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_000380045.1", "gtdb_species": "s__Streptococcus marimammalium", "ani": 87.4481, "matched_fragments": 410, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "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_000186445.1", "gtdb_species": "s__Streptococcus agalactiae", "ani": 78.4549, "matched_fragments": 87, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.63", "num_clustered_genomes": 1516, "status": "-" }, { "accession": "GCF_002096435.1", "gtdb_species": "s__Streptococcus oralis_AA", "ani": 78.3761, "matched_fragments": 58, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900475415.1", "gtdb_species": "s__Streptococcus porcinus", "ani": 78.2908, "matched_fragments": 88, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.32", "min_intra_species_ani": "99.10", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_000187935.1", "gtdb_species": "s__Streptococcus parauberis", "ani": 78.2263, "matched_fragments": 87, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.45", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_901542335.1", "gtdb_species": "s__Streptococcus porcinus_A", "ani": 78.2058, "matched_fragments": 82, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.24", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016461705.1", "gtdb_species": "s__Streptococcus vicugnae", "ani": 78.182, "matched_fragments": 102, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.43", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900104225.1", "gtdb_species": "s__Streptococcus equinus_D", "ani": 78.1744, "matched_fragments": 92, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "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_000188055.2", "gtdb_species": "s__Streptococcus urinalis", "ani": 77.9774, "matched_fragments": 106, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018448765.1", "gtdb_species": "s__Streptococcus oralis_BM", "ani": 77.9035, "matched_fragments": 67, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "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_001431045.1", "gtdb_species": "s__Streptococcus orisasini", "ani": 77.5748, "matched_fragments": 84, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "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_000411475.1", "gtdb_species": "s__Streptococcus sp000411475", "ani": 77.4749, "matched_fragments": 68, "total_fragments": 518, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.157, "cell_length": -0.167, "doubling_h": -0.216, "growth_tmp": 36.667, "optimum_tmp": 36.284, "optimum_ph": 6.89, "genome_size": 2093253.959, "gc_content": 39.262, "coding_genes": 1944.968, "rRNA16S_genes": 4.791, "tRNA_genes": 62.087, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.285, "facultative_respiration": 0.337, "anaerobic_respiration": 0.146, "aerobic_respiration": 0.516, "mesophilic_range_tmp": 0.969, "thermophilic_range_tmp": 0.03, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.943, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.056, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Streptococcus", "zalophi" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }