{ "type": "genome", "identifier": "GCF_016908645.1", "organism": "Streptococcus loxodontisalivarius", "title": "Streptococcus loxodontisalivarius", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016908645.1", "bioproject": "PRJNA224116", "biosample": "SAMN17619950", "wgs_master": "JAFBEH000000000.1", "refseq_category": "reference genome", "taxid": "1349415", "species_taxid": "1349415", "organism_name": "Streptococcus loxodontisalivarius", "infraspecific_name": "strain=DSM 27382", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/19", "asm_name": "ASM1690864v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_016908645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/908/645/GCF_016908645.1_ASM1690864v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2226923", "genome_size_ungapped": "2226923", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "95", "contig_count": "95", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016908645.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2123", "protein_coding_gene_count": "2027", "non_coding_gene_count": "50", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-19", "dateModified": "2021-02-19", "datePublished": "2021-02-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptococcus loxodontisalivarius" ], "sample_taxid": [ "1349415" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.631 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)": "2226923", "Number of Sequences": "95", "Longest Sequences (bp)": "154262", "N50 (bp)": "42850", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.7", "Number of CDSs": "2046", "Average Protein Length": "309.7", "Coding Ratio (%)": "85.4", "Number of rRNAs": "2", "Number of tRNAs": "42", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptococcus loxodontisalivarius", "strain": "strain=DSM 27382", "accession": "GCA_016908645.1", "taxid": 1349415, "species_taxid": 1349415, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 684, "total_fragments": 693, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptococcus saliviloxodontae", "strain": "strain=DSM 27513", "accession": "GCA_016908655.1", "taxid": 1349416, "species_taxid": 1349416, "relation_to_type": "type", "validated": true, "ani": 83.0415, "matched_fragments": 392, "total_fragments": 693, "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": 80.3922, "matched_fragments": 123, "total_fragments": 693, "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": 80.3111, "matched_fragments": 124, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus salivarius", "strain": "strain=JCM 5707", "accession": "GCA_019972895.1", "taxid": 1304, "species_taxid": 1304, "relation_to_type": "suspected-type", "validated": true, "ani": 80.0176, "matched_fragments": 188, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus salivarius", "strain": "strain=NCTC8618", "accession": "GCA_900636435.1", "taxid": 1304, "species_taxid": 1304, "relation_to_type": "suspected-type", "validated": true, "ani": 80.0072, "matched_fragments": 190, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus salivarius", "strain": "strain=NCTC 8618", "accession": "GCA_000785515.1", "taxid": 1304, "species_taxid": 1304, "relation_to_type": "suspected-type", "validated": true, "ani": 79.9547, "matched_fragments": 190, "total_fragments": 693, "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": 79.5253, "matched_fragments": 102, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus gallolyticus", "strain": "strain=NCTC13773", "accession": "GCA_900475715.1", "taxid": 315405, "species_taxid": 315405, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0357, "matched_fragments": 192, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus gallolyticus subsp. gallolyticus", "strain": "strain=DSM 16831", "accession": "GCA_002000985.1", "taxid": 53354, "species_taxid": 315405, "relation_to_type": "type", "validated": true, "ani": 79.0293, "matched_fragments": 189, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus equi subsp. ruminatorum", "strain": "strain=CECT 5772", "accession": "GCA_000706805.1", "taxid": 254358, "species_taxid": 1336, "relation_to_type": "type", "validated": true, "ani": 78.9939, "matched_fragments": 74, "total_fragments": 693, "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": 78.8922, "matched_fragments": 124, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus penaeicida", "strain": "strain=CAIM 1838", "accession": "GCA_002887775.1", "taxid": 1765960, "species_taxid": 1765960, "relation_to_type": "type", "validated": true, "ani": 78.6837, "matched_fragments": 127, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus ovis", "strain": "strain=DSM 16829", "accession": "GCA_000380125.1", "taxid": 82806, "species_taxid": 82806, "relation_to_type": "type", "validated": true, "ani": 78.4573, "matched_fragments": 118, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus porci", "strain": "strain=DSM 23759", "accession": "GCA_000423765.1", "taxid": 502567, "species_taxid": 502567, "relation_to_type": "type", "validated": true, "ani": 78.4189, "matched_fragments": 155, "total_fragments": 693, "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": 78.3528, "matched_fragments": 117, "total_fragments": 693, "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": 78.0008, "matched_fragments": 89, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus ruminantium", "strain": "strain=GUT187T", "accession": "GCA_003609975.1", "taxid": 1917441, "species_taxid": 1917441, "relation_to_type": "type", "validated": true, "ani": 77.9614, "matched_fragments": 91, "total_fragments": 693, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_016908645.1", "gtdb_species": "s__Streptococcus loxodontisalivarius", "ani": 100.0, "matched_fragments": 684, "total_fragments": 693, "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_016908655.1", "gtdb_species": "s__Streptococcus saliviloxodontae", "ani": 83.0502, "matched_fragments": 390, "total_fragments": 693, "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": 80.3922, "matched_fragments": 123, "total_fragments": 693, "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_000785515.1", "gtdb_species": "s__Streptococcus salivarius", "ani": 79.9379, "matched_fragments": 191, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.08", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.82", "num_clustered_genomes": 131, "status": "-" }, { "accession": "GCF_900101445.1", "gtdb_species": "s__Streptococcus equinus_B", "ani": 79.8142, "matched_fragments": 189, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.02", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_010604095.1", "gtdb_species": "s__Streptococcus sp000187445", "ani": 79.6217, "matched_fragments": 188, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.94", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.80", "num_clustered_genomes": 19, "status": "-" }, { "accession": "GCF_900104225.1", "gtdb_species": "s__Streptococcus equinus_D", "ani": 79.5018, "matched_fragments": 183, "total_fragments": 693, "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_015594605.1", "gtdb_species": "s__Streptococcus sp015594605", "ani": 79.4049, "matched_fragments": 221, "total_fragments": 693, "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_000283635.1", "gtdb_species": "s__Streptococcus macedonicus", "ani": 79.1585, "matched_fragments": 180, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 96.3165, "mean_intra_species_ani": "99.04", "min_intra_species_ani": "98.50", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCA_900478025.1", "gtdb_species": "s__Streptococcus pasteurianus", "ani": 79.0474, "matched_fragments": 175, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 96.1304, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "98.58", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_003337175.1", "gtdb_species": "s__Streptococcus gallolyticus_B", "ani": 79.0318, "matched_fragments": 180, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.6693, "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_002000985.1", "gtdb_species": "s__Streptococcus gallolyticus", "ani": 79.0294, "matched_fragments": 189, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 96.3165, "mean_intra_species_ani": "98.04", "min_intra_species_ani": "96.86", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.79", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCA_003521145.1", "gtdb_species": "s__Streptococcus sp003521145", "ani": 78.5839, "matched_fragments": 147, "total_fragments": 693, "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_902729355.1", "gtdb_species": "s__Streptococcus sp902729355", "ani": 78.5772, "matched_fragments": 165, "total_fragments": 693, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.77", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000423765.1", "gtdb_species": "s__Streptococcus porci", "ani": 78.4291, "matched_fragments": 154, "total_fragments": 693, "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": 77.637, "matched_fragments": 129, "total_fragments": 693, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.157, "cell_length": -0.167, "doubling_h": -0.216, "growth_tmp": 37.0, "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": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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", "loxodontisalivarius" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }