{ "type": "genome", "identifier": "GCF_003143695.2", "organism": "Streptococcus halitosis", "title": "Streptococcus halitosis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Human Microbiology Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003143695.2", "bioproject": "PRJNA224116", "biosample": "SAMN08929985", "wgs_master": "QEMY00000000.2", "refseq_category": "reference genome", "taxid": "2172545", "species_taxid": "2172545", "organism_name": "Streptococcus halitosis", "infraspecific_name": "strain=VT-4", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/08", "asm_name": "ASM314369v2", "asm_submitter": "Human Microbiology Institute", "gbrs_paired_asm": "GCA_003143695.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/143/695/GCF_003143695.2_ASM314369v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1880676", "genome_size_ungapped": "1880608", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "18", "contig_count": "18", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003143695.2-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "1852", "protein_coding_gene_count": "1768", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-08", "dateModified": "2018-12-08", "datePublished": "2018-12-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptococcus halitosis" ], "sample_taxid": [ "2172545" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: New York, NY" ], "sample_host_location_id": [], "data_size": "0.534 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)": "1880676", "Number of Sequences": "18", "Longest Sequences (bp)": "1331771", "N50 (bp)": "1331771", "Gap Ratio (%)": "0.003616", "GCcontent (%)": "41.0", "Number of CDSs": "1790", "Average Protein Length": "313.1", "Coding Ratio (%)": "89.4", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptococcus halitosis", "strain": "strain=VT-4", "accession": "GCA_003143695.2", "taxid": 2172545, "species_taxid": 2172545, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 621, "total_fragments": 622, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptococcus oralis", "strain": "strain=FDAARGOS_1020", "accession": "GCA_016127555.1", "taxid": 1303, "species_taxid": 1303, "relation_to_type": "type", "validated": true, "ani": 93.3362, "matched_fragments": 518, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus oralis", "strain": "strain=CCUG 13229", "accession": "GCA_002014885.1", "taxid": 1303, "species_taxid": 1303, "relation_to_type": "type", "validated": true, "ani": 93.3246, "matched_fragments": 518, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus oralis", "strain": "strain=CCUG 24891", "accession": "GCA_001639375.1", "taxid": 1303, "species_taxid": 1303, "relation_to_type": "type", "validated": true, "ani": 93.3038, "matched_fragments": 521, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus oralis", "strain": "strain=ATCC 35037", "accession": "GCA_000164095.1", "taxid": 1303, "species_taxid": 1303, "relation_to_type": "type", "validated": true, "ani": 93.2686, "matched_fragments": 517, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus oralis", "strain": "strain=ATCC 35037", "accession": "GCA_000148565.2", "taxid": 1303, "species_taxid": 1303, "relation_to_type": "type", "validated": true, "ani": 93.1865, "matched_fragments": 522, "total_fragments": 622, "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": 92.0072, "matched_fragments": 512, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus vulneris", "strain": "strain=DM3B3", "accession": "GCA_019218685.1", "taxid": 2853160, "species_taxid": 2853160, "relation_to_type": "type", "validated": true, "ani": 87.0474, "matched_fragments": 455, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus toyakuensis", "strain": "strain=TP1632", "accession": "GCA_024346585.1", "taxid": 2819619, "species_taxid": 2819619, "relation_to_type": "type", "validated": true, "ani": 86.9997, "matched_fragments": 461, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus infantis", "strain": "strain=ATCC 700779", "accession": "GCA_000187465.1", "taxid": 68892, "species_taxid": 68892, "relation_to_type": "suspected-type", "validated": true, "ani": 83.4686, "matched_fragments": 384, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus infantis", "strain": "strain=ATCC 700779", "accession": "GCA_000260755.1", "taxid": 68892, "species_taxid": 68892, "relation_to_type": "suspected-type", "validated": true, "ani": 83.3557, "matched_fragments": 371, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus peroris", "strain": "strain=ATCC 700780", "accession": "GCA_000187585.1", "taxid": 68891, "species_taxid": 68891, "relation_to_type": "type", "validated": true, "ani": 82.6605, "matched_fragments": 360, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus parasuis", "strain": "strain=SUT-286", "accession": "GCA_021654455.1", "taxid": 1501662, "species_taxid": 1501662, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0003, "matched_fragments": 114, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus oriscaviae", "strain": "strain=HKU75", "accession": "GCA_018137985.1", "taxid": 2781599, "species_taxid": 2781599, "relation_to_type": "type", "validated": true, "ani": 78.3205, "matched_fragments": 95, "total_fragments": 622, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003143695.2", "gtdb_species": "s__Streptococcus halitosis", "ani": 100.0, "matched_fragments": 621, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.61", "min_intra_species_ani": "95.24", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 11, "status": "conclusive" }, { "accession": "GCF_000257845.1", "gtdb_species": "s__Streptococcus oralis_W", "ani": 94.7764, "matched_fragments": 544, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "95.02", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.90", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCA_905221355.1", "gtdb_species": "s__Streptococcus sp905221355", "ani": 94.5327, "matched_fragments": 541, "total_fragments": 622, "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_018448765.1", "gtdb_species": "s__Streptococcus oralis_BM", "ani": 94.458, "matched_fragments": 522, "total_fragments": 622, "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": "GCA_000344275.1", "gtdb_species": "s__Streptococcus oralis_E", "ani": 94.2149, "matched_fragments": 534, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.70", "min_intra_species_ani": "95.70", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000287715.1", "gtdb_species": "s__Streptococcus oralis_Y", "ani": 94.1884, "matched_fragments": 552, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.24", "min_intra_species_ani": "95.17", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002356415.1", "gtdb_species": "s__Streptococcus oralis_F", "ani": 94.1142, "matched_fragments": 537, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.57", "min_intra_species_ani": "95.26", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_905221415.1", "gtdb_species": "s__Streptococcus sp905221415", "ani": 94.1063, "matched_fragments": 522, "total_fragments": 622, "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": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003942795.1", "gtdb_species": "s__Streptococcus mitis_BJ", "ani": 94.0515, "matched_fragments": 538, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.60", "min_intra_species_ani": "99.60", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_015561235.1", "gtdb_species": "s__Streptococcus oralis_BK", "ani": 93.7559, "matched_fragments": 529, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.42", "min_intra_species_ani": "96.42", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900637025.1", "gtdb_species": "s__Streptococcus oralis", "ani": 93.3777, "matched_fragments": 519, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.04", "min_intra_species_ani": "95.11", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.80", "num_clustered_genomes": 39, "status": "-" }, { "accession": "GCF_002386345.1", "gtdb_species": "s__Streptococcus oralis_S", "ani": 93.2441, "matched_fragments": 543, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "95.33", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_001579025.1", "gtdb_species": "s__Streptococcus oralis_X", "ani": 92.7364, "matched_fragments": 520, "total_fragments": 622, "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_000253155.1", "gtdb_species": "s__Streptococcus oralis_L", "ani": 92.7042, "matched_fragments": 530, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.38", "min_intra_species_ani": "95.38", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_905221385.1", "gtdb_species": "s__Streptococcus sp905221385", "ani": 92.6006, "matched_fragments": 501, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.72", "min_intra_species_ani": "97.71", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_905221255.1", "gtdb_species": "s__Streptococcus sp905221255", "ani": 92.4834, "matched_fragments": 510, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.55", "min_intra_species_ani": "97.53", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002096685.1", "gtdb_species": "s__Streptococcus oralis_AD", "ani": 92.1037, "matched_fragments": 514, "total_fragments": 622, "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_003943905.1", "gtdb_species": "s__Streptococcus mitis_BC", "ani": 92.0126, "matched_fragments": 508, "total_fragments": 622, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.34", "min_intra_species_ani": "95.34", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_905221365.1", "gtdb_species": "s__Streptococcus sp905221365", "ani": 91.9321, "matched_fragments": 497, "total_fragments": 622, "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_003942695.1", "gtdb_species": "s__Streptococcus mitis_BD", "ani": 91.8202, "matched_fragments": 511, "total_fragments": 622, "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": "99.98", "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", "halitosis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }