{ "type": "genome", "identifier": "GCA_000508565.1", "organism": "Streptococcus parasanguinis DORA_23_24", "title": "Streptococcus parasanguinis DORA_23_24", "description": "derived from metagenome; fragmented assembly; genome length too large", "data type": "Genome sequencing and assembly", "organization": "University of California, Berkeley", "publication": [ {} ], "properties": { "assembly_accession": "GCA_000508565.1", "bioproject": "PRJNA221495", "biosample": "SAMN02316559", "wgs_master": "AZMG00000000.1", "refseq_category": "na", "taxid": "1403947", "species_taxid": "1318", "organism_name": "Streptococcus parasanguinis DORA_23_24", "infraspecific_name": "", "isolate": "", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/12/16", "asm_name": "Strpp_DORA_23_24_velvet_1.1", "submitter": "University of California, Berkeley", "gbrs_paired_asm": "GCF_000508565.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/508/565/GCA_000508565.1_Strpp_DORA_23_24_velvet_1.1", "excluded_from_refseq": "derived from metagenome; fragmented assembly; genome length too large", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-12-16", "dateModified": "2013-12-16", "datePublished": "2013-12-16", "_annotation": { "sample_count": 1, "sample_organism": [ "human gut metagenome" ], "sample_taxid": [ "408170" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Comer Children's Hospital at the University of Chicago" ], "sample_host_location_id": [], "data_size": "0.821 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 64.96, "contamination": 27.06, "strain_heterogeneity": 64.29, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "2825308", "Number of Sequences": "1431", "Longest Sequences (bp)": "30146", "N50 (bp)": "3449", "Gap Ratio (%)": "0.131101", "GCcontent (%)": "40.7", "Number of CDSs": "1924", "Average Protein Length": "273.1", "Coding Ratio (%)": "55.8", "Number of rRNAs": "0", "Number of tRNAs": "17", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptococcus parasanguinis", "strain": "strain=ATCC 15912", "accession": "GCA_000164675.2", "taxid": 1318, "species_taxid": 1318, "relation_to_type": "suspected-type", "validated": true, "ani": 93.4885, "matched_fragments": 328, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus parasanguinis", "strain": "strain=NCTC12854", "accession": "GCA_900459355.1", "taxid": 1318, "species_taxid": 1318, "relation_to_type": "suspected-type", "validated": true, "ani": 93.4839, "matched_fragments": 329, "total_fragments": 408, "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": 83.5533, "matched_fragments": 113, "total_fragments": 408, "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": 83.4276, "matched_fragments": 114, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus australis", "strain": "strain=NCTC13166", "accession": "GCA_900476055.1", "taxid": 113107, "species_taxid": 113107, "relation_to_type": "type", "validated": true, "ani": 83.0887, "matched_fragments": 215, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus australis", "strain": "strain=ATCC 700641", "accession": "GCA_000186465.1", "taxid": 113107, "species_taxid": 113107, "relation_to_type": "type", "validated": true, "ani": 83.0605, "matched_fragments": 216, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus australis", "strain": "strain=ATCC 700641", "accession": "GCA_000222745.2", "taxid": 113107, "species_taxid": 113107, "relation_to_type": "type", "validated": true, "ani": 83.0085, "matched_fragments": 217, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus ilei", "strain": "strain=I-G2", "accession": "GCA_000479335.1", "taxid": 1156431, "species_taxid": 1156431, "relation_to_type": "type", "validated": true, "ani": 82.864, "matched_fragments": 197, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus rubneri", "strain": "strain=DSM 26920", "accession": "GCA_004785935.1", "taxid": 1234680, "species_taxid": 1234680, "relation_to_type": "type", "validated": true, "ani": 82.743, "matched_fragments": 209, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus koreensis", "strain": "strain=JS71", "accession": "GCA_003627135.1", "taxid": 2382163, "species_taxid": 2382163, "relation_to_type": "type", "validated": true, "ani": 82.6394, "matched_fragments": 206, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus timonensis", "strain": "strain=Marseille-P2915", "accession": "GCA_900095845.1", "taxid": 1852387, "species_taxid": 1852387, "relation_to_type": "type", "validated": true, "ani": 81.8028, "matched_fragments": 116, "total_fragments": 408, "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": 81.7008, "matched_fragments": 104, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus chosunense", "strain": "strain=ChDC B353", "accession": "GCA_003626515.1", "taxid": 2707003, "species_taxid": 2707003, "relation_to_type": "type", "validated": true, "ani": 80.1143, "matched_fragments": 94, "total_fragments": 408, "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": 79.7554, "matched_fragments": 95, "total_fragments": 408, "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": 79.689, "matched_fragments": 89, "total_fragments": 408, "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": 78.9631, "matched_fragments": 93, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus constellatus subsp. constellatus", "strain": "strain=CCUG 24889", "accession": "GCA_023167545.1", "taxid": 184246, "species_taxid": 76860, "relation_to_type": "type", "validated": true, "ani": 76.7546, "matched_fragments": 52, "total_fragments": 408, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 64.96, "contamination": 27.06, "strain_heterogeneity": 64.29 }, "gtdb_result": [ { "accession": "GCF_016648925.1", "gtdb_species": "s__Streptococcus sp900766505", "ani": 95.0735, "matched_fragments": 337, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.2991, "mean_intra_species_ani": "95.66", "min_intra_species_ani": "95.35", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 30, "status": "-" }, { "accession": "GCA_018365265.1", "gtdb_species": "s__Streptococcus parasanguinis_G", "ani": 94.9372, "matched_fragments": 331, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0331, "mean_intra_species_ani": "95.56", "min_intra_species_ani": "95.56", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000448565.1", "gtdb_species": "s__Streptococcus sp000448565", "ani": 94.8242, "matched_fragments": 357, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.2003, "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_000963275.1", "gtdb_species": "s__Streptococcus parasanguinis_B", "ani": 94.7443, "matched_fragments": 348, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.2991, "mean_intra_species_ani": "95.64", "min_intra_species_ani": "95.37", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_009717815.1", "gtdb_species": "s__Streptococcus parasanguinis_F", "ani": 94.7395, "matched_fragments": 336, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.25, "mean_intra_species_ani": "95.86", "min_intra_species_ani": "95.53", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.86", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCA_018366675.1", "gtdb_species": "s__Streptococcus parasanguinis_E", "ani": 94.7228, "matched_fragments": 309, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.293, "mean_intra_species_ani": "95.61", "min_intra_species_ani": "95.45", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_001813295.1", "gtdb_species": "s__Streptococcus sp001813295", "ani": 94.6702, "matched_fragments": 332, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.2593, "mean_intra_species_ani": "95.62", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.87", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001073155.1", "gtdb_species": "s__Streptococcus parasanguinis_D", "ani": 94.4888, "matched_fragments": 322, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.84", "min_intra_species_ani": "96.67", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_000180035.1", "gtdb_species": "s__Streptococcus parasanguinis_C", "ani": 94.3226, "matched_fragments": 332, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.27", "min_intra_species_ani": "96.01", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001074805.1", "gtdb_species": "s__Streptococcus parasanguinis_A", "ani": 93.5942, "matched_fragments": 336, "total_fragments": 408, "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_000164675.2", "gtdb_species": "s__Streptococcus parasanguinis", "ani": 93.4885, "matched_fragments": 328, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.96", "min_intra_species_ani": "95.18", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCA_902373455.1", "gtdb_species": "s__Streptococcus sp902373455", "ani": 93.3338, "matched_fragments": 218, "total_fragments": 408, "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_900755085.1", "gtdb_species": "s__Streptococcus sp900755085", "ani": 91.5056, "matched_fragments": 277, "total_fragments": 408, "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_001074155.1", "gtdb_species": "s__Streptococcus pseudopneumoniae_A", "ani": 83.946, "matched_fragments": 107, "total_fragments": 408, "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_000223335.1", "gtdb_species": "s__Streptococcus infantis_H", "ani": 83.8607, "matched_fragments": 115, "total_fragments": 408, "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_000187465.1", "gtdb_species": "s__Streptococcus infantis", "ani": 83.5533, "matched_fragments": 113, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_015546995.1", "gtdb_species": "s__Streptococcus infantis_J", "ani": 83.3518, "matched_fragments": 113, "total_fragments": 408, "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_000279535.1", "gtdb_species": "s__Streptococcus infantis_I", "ani": 82.8982, "matched_fragments": 115, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.10", "min_intra_species_ani": "95.79", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_000223255.2", "gtdb_species": "s__Streptococcus infantis_G", "ani": 82.7765, "matched_fragments": 108, "total_fragments": 408, "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": 82.3509, "matched_fragments": 111, "total_fragments": 408, "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": "-" }, { "accession": "GCF_000215385.1", "gtdb_species": "s__Streptococcus infantis_B", "ani": 82.3113, "matched_fragments": 111, "total_fragments": 408, "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_001075875.1", "gtdb_species": "s__Streptococcus oralis_I", "ani": 82.1232, "matched_fragments": 106, "total_fragments": 408, "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_001072375.1", "gtdb_species": "s__Streptococcus pseudopneumoniae_L", "ani": 81.7627, "matched_fragments": 96, "total_fragments": 408, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.33", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001579645.1", "gtdb_species": "s__Streptococcus infantis_E", "ani": 81.5429, "matched_fragments": 102, "total_fragments": 408, "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": -0.097, "cell_length": -0.097, "doubling_h": -0.216, "growth_tmp": 37.0, "optimum_tmp": 36.284, "optimum_ph": 6.89, "genome_size": 2226691.471, "gc_content": 41.463, "coding_genes": 1976.4, "rRNA16S_genes": 4.0, "tRNA_genes": 61.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.285, "facultative_respiration": 0.0, "anaerobic_respiration": 1.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__Streptococcus parasanguinis_I" ], "_genome_taxon": [ "Streptococcus", "parasanguinis", "DORA_23_24", "d__Bacteria", "p__Bacillota", "c__Bacilli", "o__Lactobacillales", "f__Streptococcaceae", "g__Streptococcus", "s__Streptococcus parasanguinis_I", "Bacteria", "Bacillota", "Bacilli", "Lactobacillales", "Streptococcaceae", "Streptococcus", "Streptococcus", "parasanguinis", "I" ], "_meo": [ { "id": "MEO_0000054", "label": "feces" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }