{ "type": "genome", "identifier": "GCF_000425665.1", "organism": "Gemella cuniculi DSM 15828", "title": "Gemella cuniculi DSM 15828", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000425665.1", "bioproject": "PRJNA224116", "biosample": "SAMN02440633", "wgs_master": "AUDW00000000.1", "refseq_category": "reference genome", "taxid": "1121914", "species_taxid": "150240", "organism_name": "Gemella cuniculi DSM 15828", "infraspecific_name": "strain=DSM 15828", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/07/11", "asm_name": "ASM42566v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000425665.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/425/665/GCF_000425665.1_ASM42566v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1869681", "genome_size_ungapped": "1864820", "gc_percent": "29.000000", "replicon_count": "0", "scaffold_count": "31", "contig_count": "39", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000425665.1-RS_2024_05_02", "annotation_date": "2024-05-02", "total_gene_count": "1736", "protein_coding_gene_count": "1669", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-07-11", "dateModified": "2013-07-11", "datePublished": "2013-07-11", "_annotation": { "sample_count": 1, "sample_organism": [ "Gemella cuniculi DSM 15828" ], "sample_taxid": [ "1121914" ], "sample_host_organism": [ "Oryctolagus cuniculus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.513 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)": "1869681", "Number of Sequences": "31", "Longest Sequences (bp)": "311847", "N50 (bp)": "82178", "Gap Ratio (%)": "0.259991", "GCcontent (%)": "29.0", "Number of CDSs": "1657", "Average Protein Length": "309.1", "Coding Ratio (%)": "82.2", "Number of rRNAs": "6", "Number of tRNAs": "41", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Gemella cuniculi", "strain": "strain=DSM 15828", "accession": "GCA_000425665.1", "taxid": 150240, "species_taxid": 150240, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 601, "total_fragments": 607, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Gemella morbillorum", "strain": "strain=NCTC11323", "accession": "GCA_900476045.1", "taxid": 29391, "species_taxid": 29391, "relation_to_type": "type", "validated": true, "ani": 79.9178, "matched_fragments": 318, "total_fragments": 607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemella morbillorum", "strain": "strain=FDAARGOS_1501", "accession": "GCA_020097435.1", "taxid": 29391, "species_taxid": 29391, "relation_to_type": "type", "validated": true, "ani": 79.8908, "matched_fragments": 319, "total_fragments": 607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemella sanguinis", "strain": "strain=ATCC 700632", "accession": "GCA_000701685.1", "taxid": 84135, "species_taxid": 84135, "relation_to_type": "type", "validated": true, "ani": 79.5489, "matched_fragments": 312, "total_fragments": 607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemella haemolysans", "strain": "strain=ATCC 10379", "accession": "GCA_000173915.1", "taxid": 1379, "species_taxid": 1379, "relation_to_type": "suspected-type", "validated": true, "ani": 79.3551, "matched_fragments": 262, "total_fragments": 607, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Gemella haemolysans", "strain": "strain=CCUG 37985T", "accession": "GCA_008692995.1", "taxid": 1379, "species_taxid": 1379, "relation_to_type": "suspected-type", "validated": true, "ani": 79.3387, "matched_fragments": 259, "total_fragments": 607, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000425665.1", "gtdb_species": "s__Gemella cuniculi", "ani": 100.0, "matched_fragments": 601, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "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_900476045.1", "gtdb_species": "s__Gemella morbillorum", "ani": 79.9711, "matched_fragments": 314, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "96.86", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCA_002871655.1", "gtdb_species": "s__Gemella sp002871655", "ani": 79.7817, "matched_fragments": 293, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000701685.1", "gtdb_species": "s__Gemella sanguinis", "ani": 79.5489, "matched_fragments": 312, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.27", "min_intra_species_ani": "96.22", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_901873445.1", "gtdb_species": "s__Gemella haemolysans_C", "ani": 79.5435, "matched_fragments": 274, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "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_001553035.1", "gtdb_species": "s__Gemella haemolysans_B", "ani": 79.3763, "matched_fragments": 264, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.70", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.81", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000173915.1", "gtdb_species": "s__Gemella haemolysans", "ani": 79.3653, "matched_fragments": 262, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_012273215.1", "gtdb_species": "s__Gemella haemolysans_A", "ani": 79.3339, "matched_fragments": 289, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900766305.1", "gtdb_species": "s__Gemella sp900766305", "ani": 79.2723, "matched_fragments": 262, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "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_900555985.1", "gtdb_species": "s__Gemella sp900555985", "ani": 78.7929, "matched_fragments": 201, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "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_013415365.1", "gtdb_species": "s__Gemella sp004570485", "ani": 78.3673, "matched_fragments": 69, "total_fragments": 607, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Gemellaceae;g__Gemella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.83", "min_intra_species_ani": "99.74", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": -0.302, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": null, "optimum_ph": null, "genome_size": 1686725.866, "gc_content": 30.413, "coding_genes": 1602.0, "rRNA16S_genes": null, "tRNA_genes": 42.0, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.75, "range_salinity": null, "facultative_respiration": 0.5, "anaerobic_respiration": 0.166, "aerobic_respiration": 0.333, "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 }, "_genome_taxon": [ "Gemella", "cuniculi", "DSM", "15828" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }