{ "type": "genome", "identifier": "GCF_900460315.1", "organism": "Veillonella criceti", "title": "Veillonella criceti", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900460315.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4412707", "wgs_master": "UHIO00000000.1", "refseq_category": "reference genome", "taxid": "103891", "species_taxid": "103891", "organism_name": "Veillonella criceti", "infraspecific_name": "strain=NCTC12020", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/01", "asm_name": "51395_D01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900460315.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/460/315/GCF_900460315.1_51395_D01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2245419", "genome_size_ungapped": "2245419", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "5", "contig_count": "5", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900460315.1-RS_2024_04_07", "annotation_date": "2024-04-07", "total_gene_count": "2036", "protein_coding_gene_count": "1945", "non_coding_gene_count": "72", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-01", "dateModified": "2018-08-01", "datePublished": "2018-08-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Veillonella criceti" ], "sample_taxid": [ "103891" ], "sample_host_organism": [ "Hamster" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "0.629 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)": "2245419", "Number of Sequences": "5", "Longest Sequences (bp)": "2205619", "N50 (bp)": "2205619", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.4", "Number of CDSs": "1989", "Average Protein Length": "327.7", "Coding Ratio (%)": "87.1", "Number of rRNAs": "15", "Number of tRNAs": "52", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Veillonella criceti", "strain": "strain=NCTC12020", "accession": "GCA_900460315.1", "taxid": 103891, "species_taxid": 103891, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 742, "total_fragments": 745, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Veillonella seminalis", "strain": "strain=ADV4313-2", "accession": "GCA_003992065.1", "taxid": 1502943, "species_taxid": 1502943, "relation_to_type": "type", "validated": true, "ani": 80.6916, "matched_fragments": 328, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella ratti", "strain": "strain=ATCC 17746", "accession": "GCA_003992115.1", "taxid": 103892, "species_taxid": 103892, "relation_to_type": "suspected-type", "validated": true, "ani": 80.3655, "matched_fragments": 340, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella parvula", "strain": "strain=DSM 2008", "accession": "GCA_000024945.1", "taxid": 29466, "species_taxid": 29466, "relation_to_type": "suspected-type", "validated": true, "ani": 78.92, "matched_fragments": 122, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella atypica", "strain": "strain=ATCC 17744", "accession": "GCA_002959915.1", "taxid": 39777, "species_taxid": 39777, "relation_to_type": "type", "validated": true, "ani": 78.7684, "matched_fragments": 113, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella nakazawae", "strain": "strain=T1-7", "accession": "GCA_013393365.1", "taxid": 2682456, "species_taxid": 2682456, "relation_to_type": "type", "validated": true, "ani": 78.7093, "matched_fragments": 137, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella rogosae", "strain": "strain=JCM 15642", "accession": "GCA_002959775.1", "taxid": 423477, "species_taxid": 423477, "relation_to_type": "type", "validated": true, "ani": 78.5256, "matched_fragments": 118, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella infantium", "strain": "strain=T11011-4", "accession": "GCA_002959895.1", "taxid": 1911679, "species_taxid": 1911679, "relation_to_type": "type", "validated": true, "ani": 78.3578, "matched_fragments": 122, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella magna", "strain": "strain=DSM 19857", "accession": "GCA_000428745.1", "taxid": 464322, "species_taxid": 464322, "relation_to_type": "type", "validated": true, "ani": 78.2809, "matched_fragments": 132, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella tobetsuensis", "strain": "strain=ATCC BAA-2400", "accession": "GCA_001078375.1", "taxid": 1110546, "species_taxid": 1110546, "relation_to_type": "type", "validated": true, "ani": 78.1937, "matched_fragments": 113, "total_fragments": 745, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella rogosae", "strain": "strain=JCM 15642", "accession": "GCA_001312485.1", "taxid": 423477, "species_taxid": 423477, "relation_to_type": 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"mean_intra_species_ani": "99.32", "min_intra_species_ani": "99.06", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_003992115.1", "gtdb_species": "s__Veillonella_A ratti", "ani": 80.3943, "matched_fragments": 340, "total_fragments": 745, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A", "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_015058545.1", "gtdb_species": "s__Veillonella_A sp015058545", "ani": 80.0356, "matched_fragments": 298, "total_fragments": 745, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_002959775.1", "gtdb_species": "s__Veillonella rogosae", "ani": 78.5229, "matched_fragments": 117, "total_fragments": 745, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.92", "min_intra_species_ani": "95.91", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.87", "num_clustered_genomes": 12, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.353, "cell_length": -0.362, "doubling_h": null, "growth_tmp": 37.0, "optimum_tmp": 36.714, "optimum_ph": 7.0, "genome_size": 2104897.156, "gc_content": 40.198, "coding_genes": 1805.666, "rRNA16S_genes": 4.0, "tRNA_genes": 48.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "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 }, "_genome_taxon": [ "Veillonella", "criceti" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }