{ "type": "genome", "identifier": "GCF_000347915.1", "organism": "Streptococcus ratti FA-1 = DSM 20564", "title": "Streptococcus ratti FA-1 = DSM 20564", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Bioprocess and Biosystems Engineering", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000347915.1", "bioproject": "PRJNA224116", "biosample": "SAMN02469961", "wgs_master": "AOCD00000000.1", "refseq_category": "na", "taxid": "699248", "species_taxid": "1341", "organism_name": "Streptococcus ratti FA-1 = DSM 20564", "infraspecific_name": "strain=DSM 20564", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/03/21", "asm_name": "DSM20564_V1", "asm_submitter": "Institute of Bioprocess and Biosystems Engineering", "gbrs_paired_asm": "GCA_000347915.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/347/915/GCF_000347915.1_DSM20564_V1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2037184", "genome_size_ungapped": "2037184", "gc_percent": "41.000000", "replicon_count": "0", "scaffold_count": "182", "contig_count": "182", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-03", "total_gene_count": "2009", "protein_coding_gene_count": "1905", "non_coding_gene_count": "38", "pubmed_id": "23805886" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-03-21", "dateModified": "2013-03-21", "datePublished": "2013-03-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptococcus ratti FA-1 = DSM 20564" ], "sample_taxid": [ "699248" ], "sample_host_organism": [ "rat" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.581 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)": "2037184", "Number of Sequences": "182", "Longest Sequences (bp)": "63218", "N50 (bp)": "23860", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.8", "Number of CDSs": "1907", "Average Protein Length": "301.3", "Coding Ratio (%)": "84.6", "Number of rRNAs": "0", "Number of tRNAs": "27", "Number of CRISPRs": "5" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptococcus ratti", "strain": "strain=DSM 20564", "accession": "GCA_000347915.1", "taxid": 1341, "species_taxid": 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80.1614, "matched_fragments": 151, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus troglodytae", "strain": "strain=TKU 31", "accession": "GCA_002355215.1", "taxid": 1111760, "species_taxid": 1111760, "relation_to_type": "type", "validated": true, "ani": 79.9717, "matched_fragments": 325, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus mutans", "strain": "strain=DSM 20523", "accession": "GCA_000375505.1", "taxid": 1309, "species_taxid": 1309, "relation_to_type": "type", "validated": true, "ani": 79.8978, "matched_fragments": 340, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus mutans", "strain": "strain=NCTC10449", "accession": "GCA_900475095.1", "taxid": 1309, "species_taxid": 1309, "relation_to_type": "type", "validated": true, "ani": 79.8826, "matched_fragments": 338, "total_fragments": 597, "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": 78.6253, "matched_fragments": 56, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus hyovaginalis", "strain": "strain=DSM 12219", "accession": "GCA_000420785.1", "taxid": 149015, "species_taxid": 149015, "relation_to_type": "type", "validated": true, "ani": 78.3391, "matched_fragments": 63, "total_fragments": 597, "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": 78.1588, "matched_fragments": 65, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus pyogenes", "strain": "strain=PartK-Spyogenes-RM8376", "accession": "GCA_022869605.1", "taxid": 1314, "species_taxid": 1314, "relation_to_type": "type", "validated": true, "ani": 78.1044, "matched_fragments": 73, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus halotolerans", "strain": "strain=HTS9", "accession": "GCA_001598035.1", "taxid": 1814128, "species_taxid": 1814128, "relation_to_type": "type", "validated": true, "ani": 77.9014, "matched_fragments": 67, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus parauberis", "strain": "strain=NCFD 2020", "accession": "GCA_000187935.2", "taxid": 1348, "species_taxid": 1348, "relation_to_type": "type", "validated": true, "ani": 77.8965, "matched_fragments": 66, "total_fragments": 597, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": 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"mean_intra_species_ani": "99.59", "min_intra_species_ani": "98.38", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.87", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_001937065.1", "gtdb_species": "s__Streptococcus sp001937065", "ani": 90.4725, "matched_fragments": 503, "total_fragments": 597, "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": 85.9401, "matched_fragments": 478, "total_fragments": 597, "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", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002355215.1", "gtdb_species": "s__Streptococcus troglodytae", "ani": 79.9717, "matched_fragments": 325, "total_fragments": 597, "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_006739205.1", "gtdb_species": "s__Streptococcus mutans", "ani": 79.97, "matched_fragments": 336, "total_fragments": 597, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.12", "min_intra_species_ani": "98.73", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.87", "num_clustered_genomes": 261, 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