{ "type": "genome", "identifier": "GCF_002959855.1", "organism": "Veillonella denticariosi JCM 15641", "title": "Veillonella denticariosi JCM 15641", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Health Sciences University of Hokkaido", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002959855.1", "bioproject": "PRJNA224116", "biosample": "SAMD00090155", "wgs_master": "PPDB00000000.1", "refseq_category": "reference genome", "taxid": "1298594", "species_taxid": "419208", "organism_name": "Veillonella denticariosi JCM 15641", "infraspecific_name": "strain=JCM 15641", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/02/27", "asm_name": "ASM295985v1", "asm_submitter": "Health Sciences University of Hokkaido", "gbrs_paired_asm": "GCA_002959855.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/959/855/GCF_002959855.1_ASM295985v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1981866", "genome_size_ungapped": "1981866", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002959855.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "1850", "protein_coding_gene_count": "1769", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-02-27", "dateModified": "2018-02-27", "datePublished": "2018-02-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Veillonella denticariosi JCM 15641" ], "sample_taxid": [ "1298594" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "0.563 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "1981866", "Number of Sequences": "8", "Longest Sequences (bp)": "800621", "N50 (bp)": "600371", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.9", "Number of CDSs": "1810", "Average Protein Length": "322.4", "Coding Ratio (%)": "88.3", "Number of rRNAs": "6", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Veillonella denticariosi", "strain": "strain=JCM 15641", "accession": "GCA_002959855.1", "taxid": 419208, "species_taxid": 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"total_fragments": 657, "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": 81.4614, "matched_fragments": 392, "total_fragments": 657, "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": 81.1925, "matched_fragments": 385, "total_fragments": 657, "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": 77.2713, "matched_fragments": 84, "total_fragments": 657, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002959855.1", "gtdb_species": "s__Veillonella denticariosi", "ani": 100.0, "matched_fragments": 657, "total_fragments": 657, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.3196, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "97.05", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_900187285.1", "gtdb_species": "s__Veillonella rodentium", "ani": 95.2827, "matched_fragments": 597, "total_fragments": 657, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.3196, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", 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