{ "type": "genome", "identifier": "GCF_001679535.1", "organism": "Streptococcus pneumoniae", "title": "Streptococcus pneumoniae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "TAILORED-Treatment project", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001679535.1", "bioproject": "PRJNA224116", "biosample": "SAMN04407280", "wgs_master": "LQXF00000000.1", "refseq_category": "na", "taxid": "1313", "species_taxid": "1313", "organism_name": "Streptococcus pneumoniae", "infraspecific_name": "strain=CCUG 28588", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/07/05", "asm_name": "ASM167953v1", "asm_submitter": "TAILORED-Treatment project", "gbrs_paired_asm": "GCA_001679535.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/679/535/GCF_001679535.1_ASM167953v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2043199", "genome_size_ungapped": "2041649", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "98", "contig_count": "98", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001679535.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "2124", "protein_coding_gene_count": "1893", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-07-05", "dateModified": "2016-07-05", "datePublished": "2016-07-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptococcus pneumoniae" ], "sample_taxid": [ "1313" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "Unknown" ], "sample_host_disease_id": [], "sample_host_location": [ "Unknown" ], "sample_host_location_id": [], "data_size": "0.583 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)": "2043199", "Number of Sequences": "98", "Longest Sequences (bp)": "170753", "N50 (bp)": "48585", "Gap Ratio (%)": "0.084280", "GCcontent (%)": "39.7", "Number of CDSs": "2017", "Average Protein Length": "288.6", "Coding Ratio (%)": "85.5", "Number of rRNAs": "3", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptococcus pneumoniae", "strain": "strain=CCUG 28588", "accession": "GCA_001679535.1", "taxid": 1313, "species_taxid": 1313, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 638, "total_fragments": 645, 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{ "organism_name": "Streptococcus toyakuensis", "strain": "strain=TP1632", "accession": "GCA_024346585.1", "taxid": 2819619, "species_taxid": 2819619, "relation_to_type": "type", "validated": true, "ani": 91.9616, "matched_fragments": 492, "total_fragments": 645, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus mitis", "strain": "strain=NCTC 12261", "accession": "GCA_000148585.3", "taxid": 28037, "species_taxid": 28037, "relation_to_type": "suspected-type", "validated": true, "ani": 91.8106, "matched_fragments": 478, "total_fragments": 645, "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": 91.6193, "matched_fragments": 498, "total_fragments": 645, "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": 91.4172, "matched_fragments": 466, "total_fragments": 645, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus gwangjuense", "strain": "strain=ChDC B345", "accession": "GCA_003627155.1", "taxid": 1433513, "species_taxid": 1433513, "relation_to_type": "type", "validated": true, "ani": 91.2836, "matched_fragments": 475, "total_fragments": 645, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus symci", "strain": "strain=C17", "accession": "GCA_006385165.1", "taxid": 2588991, "species_taxid": 2588991, "relation_to_type": "type", "validated": true, "ani": 91.2779, "matched_fragments": 460, "total_fragments": 645, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus chosunense", "strain": "strain=ChDC B353", "accession": 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1501662, "species_taxid": 1501662, "relation_to_type": "suspected-type", "validated": true, "ani": 78.7258, "matched_fragments": 117, "total_fragments": 645, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001457635.1", "gtdb_species": "s__Streptococcus pneumoniae", "ani": 99.9741, "matched_fragments": 644, "total_fragments": 645, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.62", "min_intra_species_ani": "97.54", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.81", "num_clustered_genomes": 8452, "status": "conclusive" }, { "accession": "GCF_002087075.1", "gtdb_species": "s__Streptococcus pseudopneumoniae", "ani": 94.4935, "matched_fragments": 513, "total_fragments": 645, "gtdb_taxonomy": 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