{ "type": "genome", "identifier": "GCA_015264635.1", "organism": "Veillonella sp.", "title": "Veillonella sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "J. Craig Venter Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCA_015264635.1", "bioproject": "PRJNA624185", "biosample": "SAMN14571074", "wgs_master": "JABZZL000000000.1", "refseq_category": "na", "taxid": "1926307", "species_taxid": "1926307", "organism_name": "Veillonella sp.", "infraspecific_name": "", "isolate": "JCVI_10_bin.7", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/11/06", "asm_name": "ASM1526463v1", "submitter": "J. Craig Venter Institute", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/015/264/635/GCA_015264635.1_ASM1526463v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-11-06", "dateModified": "2020-11-06", "datePublished": "2020-11-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Veillonella sp." ], "sample_taxid": [ "1926307" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: UCLA School of Dentistry" ], "sample_host_location_id": [], "data_size": "0.438 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 82.41, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1494829", "Number of Sequences": "454", "Longest Sequences (bp)": "30106", "N50 (bp)": "4402", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.1", "Number of CDSs": "1043", "Average Protein Length": "293.4", "Coding Ratio (%)": "61.4", "Number of rRNAs": "0", "Number of tRNAs": "8", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Veillonella atypica", "strain": "strain=ATCC 17744", "accession": "GCA_002959915.1", "taxid": 39777, "species_taxid": 39777, "relation_to_type": "type", "validated": true, "ani": 97.3548, "matched_fragments": 241, "total_fragments": 256, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Veillonella atypica", "strain": "strain=NCTC11830", "accession": "GCA_900460235.1", "taxid": 39777, "species_taxid": 39777, "relation_to_type": "type", "validated": true, "ani": 97.3517, "matched_fragments": 241, "total_fragments": 256, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Veillonella atypica", "strain": "strain=KON", "accession": "GCA_000318355.2", "taxid": 39777, "species_taxid": 39777, "relation_to_type": "type", "validated": true, "ani": 97.2948, "matched_fragments": 240, "total_fragments": 256, "ani_threshold": 95, "status": "conclusive" }, { "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": 88.0858, "matched_fragments": 234, "total_fragments": 256, "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": 83.6171, "matched_fragments": 176, "total_fragments": 256, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella dispar", "strain": "strain=NCTC11831", "accession": "GCA_900637515.1", "taxid": 39778, "species_taxid": 39778, "relation_to_type": "suspected-type", "validated": true, "ani": 83.255, "matched_fragments": 177, "total_fragments": 256, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella dispar", "strain": "strain=ATCC 17748", "accession": "GCA_000160015.1", "taxid": 39778, "species_taxid": 39778, "relation_to_type": "suspected-type", "validated": true, "ani": 83.213, "matched_fragments": 176, "total_fragments": 256, "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": 82.1321, "matched_fragments": 167, "total_fragments": 256, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Veillonella caviae", "strain": "strain=DSM 20738", "accession": "GCA_003992125.1", "taxid": 248316, "species_taxid": 248316, "relation_to_type": "type", "validated": true, "ani": 80.8411, "matched_fragments": 147, "total_fragments": 256, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 82.41, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002959915.1", "gtdb_species": "s__Veillonella atypica", "ani": 97.3548, "matched_fragments": 241, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.10", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.87", "num_clustered_genomes": 34, "status": "conclusive" }, { "accession": "GCA_905214495.1", "gtdb_species": "s__Veillonella sp905214495", "ani": 94.7134, "matched_fragments": 187, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "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_001078375.1", "gtdb_species": "s__Veillonella tobetsuensis", "ani": 88.0858, "matched_fragments": 234, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.55", "min_intra_species_ani": "97.11", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_900637515.1", "gtdb_species": "s__Veillonella dispar", "ani": 83.255, "matched_fragments": 177, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.54", "min_intra_species_ani": "95.48", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_002959755.1", "gtdb_species": "s__Veillonella sp002959755", "ani": 83.1274, "matched_fragments": 178, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "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_900549845.1", "gtdb_species": "s__Veillonella sp900549845", "ani": 82.3757, "matched_fragments": 125, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "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_905209685.1", "gtdb_species": "s__Veillonella sp905209685", "ani": 81.9877, "matched_fragments": 151, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.07", "min_intra_species_ani": "95.07", "mean_intra_species_af": "0.78", "min_intra_species_af": "0.78", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900765235.1", "gtdb_species": "s__Veillonella sp900765235", "ani": 81.7483, "matched_fragments": 117, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "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_902834965.1", "gtdb_species": "s__Veillonella sp902834965", "ani": 81.7273, "matched_fragments": 91, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "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_003992125.1", "gtdb_species": "s__Veillonella caviae", "ani": 80.8411, "matched_fragments": 147, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "98.44", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_009929605.1", "gtdb_species": "s__Veillonella sp009929605", "ani": 79.5902, "matched_fragments": 88, "total_fragments": 256, "gtdb_taxonomy": "d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Veillonellaceae;g__Veillonella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.43", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.82", "num_clustered_genomes": 7, "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 }, "_gtdb_taxon": [ "d__Bacteria", "p__Bacillota_C", "c__Negativicutes", "o__Veillonellales", "f__Veillonellaceae", "g__Veillonella", "s__Veillonella atypica" ], "_genome_taxon": [ "Veillonella", "sp.", "d__Bacteria", "p__Bacillota_C", "c__Negativicutes", "o__Veillonellales", "f__Veillonellaceae", "g__Veillonella", "s__Veillonella atypica", "Bacteria", "Bacillota", "C", "Negativicutes", "Veillonellales", "Veillonellaceae", "Veillonella", "Veillonella", "atypica" ], "_meo": [ { "id": "MEO_0000060", "label": "saliva" } ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }