{ "type": "genome", "identifier": "GCF_001885095.1", "organism": "Streptococcus bovimastitidis", "title": "Streptococcus bovimastitidis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Cambridge", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001885095.1", "bioproject": "PRJNA224116", "biosample": "SAMN05199910", "wgs_master": "LZDD00000000.1", "refseq_category": "reference genome", "taxid": "1856638", "species_taxid": "1856638", "organism_name": "Streptococcus bovimastitidis", "infraspecific_name": "strain=NZ1587", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/21", "asm_name": "ASM188509v1", "asm_submitter": "University of Cambridge", "gbrs_paired_asm": "GCA_001885095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/885/095/GCF_001885095.1_ASM188509v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2075036", "genome_size_ungapped": "2075036", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001885095.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2127", "protein_coding_gene_count": "2038", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-21", "dateModified": "2016-11-21", "datePublished": "2016-11-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Streptococcus bovimastitidis" ], "sample_taxid": [ "1856638" ], "sample_host_organism": [ "Bos taurus" ], "sample_host_organism_id": [], "sample_host_disease": [ "Mastitis" ], "sample_host_disease_id": [], "sample_host_location": [ "New Zealand: Motumaoho" ], "sample_host_location_id": [], "data_size": "0.585 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)": "2075036", "Number of Sequences": "8", "Longest Sequences (bp)": "1134340", "N50 (bp)": "1134340", "Gap Ratio (%)": "0.000096", "GCcontent (%)": "37.3", "Number of CDSs": "2079", "Average Protein Length": "296.1", "Coding Ratio (%)": "89.0", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Streptococcus bovimastitidis", "strain": "strain=NZ1587", "accession": "GCA_001885095.1", "taxid": 1856638, "species_taxid": 1856638, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 689, "total_fragments": 689, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Streptococcus penaeicida", "strain": "strain=CAIM 1838", "accession": "GCA_002887775.1", "taxid": 1765960, "species_taxid": 1765960, "relation_to_type": "type", "validated": true, "ani": 93.2269, "matched_fragments": 558, "total_fragments": 689, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus uberis", "strain": "strain=NCTC3858", "accession": "GCA_900475595.1", "taxid": 1349, "species_taxid": 1349, "relation_to_type": "type", "validated": true, "ani": 81.0245, "matched_fragments": 331, "total_fragments": 689, "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": 80.8488, "matched_fragments": 283, "total_fragments": 689, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus porcinus", "strain": "strain=NCTC10999", "accession": "GCA_900475415.1", "taxid": 1340, "species_taxid": 1340, "relation_to_type": "type", "validated": true, "ani": 80.6652, "matched_fragments": 326, "total_fragments": 689, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus pseudoporcinus", "strain": "strain=NCTC13786", "accession": "GCA_900637075.1", "taxid": 361101, "species_taxid": 361101, "relation_to_type": "type", "validated": true, "ani": 80.2873, "matched_fragments": 340, "total_fragments": 689, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus pseudoporcinus", "strain": "strain=LQ 940-04", "accession": "GCA_000188035.3", "taxid": 361101, "species_taxid": 361101, "relation_to_type": "type", "validated": true, "ani": 80.2483, "matched_fragments": 346, "total_fragments": 689, "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": 79.853, "matched_fragments": 191, "total_fragments": 689, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus canis", "strain": "strain=NCTC12191", "accession": "GCA_900636575.1", "taxid": 1329, "species_taxid": 1329, "relation_to_type": "type", "validated": true, "ani": 79.3294, "matched_fragments": 181, "total_fragments": 689, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Streptococcus henryi", "strain": "strain=DSM 19005", "accession": "GCA_000376985.1", "taxid": 439219, "species_taxid": 439219, "relation_to_type": "type", "validated": true, "ani": 79.1492, "matched_fragments": 130, "total_fragments": 689, "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": 79.0054, "matched_fragments": 79, "total_fragments": 689, "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": 78.5057, "matched_fragments": 86, "total_fragments": 689, "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": 78.3184, "matched_fragments": 98, "total_fragments": 689, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001885095.1", "gtdb_species": "s__Streptococcus bovimastitidis", "ani": 100.0, "matched_fragments": 689, "total_fragments": 689, "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_002887775.1", "gtdb_species": "s__Streptococcus penaeicida", "ani": 93.2269, "matched_fragments": 558, "total_fragments": 689, "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_900475595.1", "gtdb_species": "s__Streptococcus uberis", "ani": 81.0245, "matched_fragments": 331, "total_fragments": 689, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.97", "min_intra_species_ani": "98.11", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 68, "status": "-" }, { "accession": "GCF_000187935.1", "gtdb_species": "s__Streptococcus parauberis", "ani": 80.8488, "matched_fragments": 283, "total_fragments": 689, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.45", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 24, "status": "-" }, { "accession": "GCF_901542335.1", "gtdb_species": "s__Streptococcus porcinus_A", 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"total_fragments": 689, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.36", "min_intra_species_ani": "97.79", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.85", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_000785785.1", "gtdb_species": "s__Streptococcus uberis_A", "ani": 79.6947, "matched_fragments": 233, "total_fragments": 689, "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_000380005.1", "gtdb_species": "s__Streptococcus didelphis", "ani": 79.6874, "matched_fragments": 199, "total_fragments": 689, "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_900636575.1", "gtdb_species": "s__Streptococcus canis", "ani": 79.3294, "matched_fragments": 181, "total_fragments": 689, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.95", "min_intra_species_ani": "97.68", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.86", "num_clustered_genomes": 20, "status": "-" }, { "accession": "GCF_000188015.2", "gtdb_species": "s__Streptococcus ictaluri", "ani": 79.2823, "matched_fragments": 191, "total_fragments": 689, "gtdb_taxonomy": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Streptococcus", "bovimastitidis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }