{ "type": "genome", "identifier": "GCF_900445775.1", "organism": "Bordetella holmesii", "title": "Bordetella holmesii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900445775.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4504060", "wgs_master": "UFTX00000000.1", "refseq_category": "na", "taxid": "35814", "species_taxid": "35814", "organism_name": "Bordetella holmesii", "infraspecific_name": "strain=NCTC12912", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/08", "asm_name": "51726_B01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900445775.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/445/775/GCF_900445775.1_51726_B01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3780341", "genome_size_ungapped": "3780341", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "6", "contig_count": "6", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900445775.1-RS_2024_08_16", "annotation_date": "2024-08-16", "total_gene_count": "3677", "protein_coding_gene_count": "3293", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-08", "dateModified": "2018-08-08", "datePublished": "2018-08-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Bordetella holmesii" ], "sample_taxid": [ "35814" ], "sample_host_organism": [ "Human (Male)" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [ "USA: New York" ], "sample_host_location_id": [], "data_size": "1.048 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)": "3780341", "Number of Sequences": "6", "Longest Sequences (bp)": "3275926", "N50 (bp)": "3275926", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "62.7", "Number of CDSs": "3766", "Average Protein Length": "301.7", "Coding Ratio (%)": "90.2", "Number of rRNAs": "9", "Number of tRNAs": "58", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bordetella holmesii", "strain": "strain=NCTC12912", "accession": "GCA_900445775.1", "taxid": 35814, "species_taxid": 35814, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1249, "total_fragments": 1257, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bordetella holmesii", "strain": "strain=FDAARGOS_1539", "accession": "GCA_020735985.1", "taxid": 35814, "species_taxid": 35814, "relation_to_type": "type", "validated": true, "ani": 99.9978, "matched_fragments": 1228, "total_fragments": 1257, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Bordetella pseudohinzii", "strain": "strain=8-296-03", "accession": "GCA_000657795.2", "taxid": 1331258, "species_taxid": 1331258, "relation_to_type": "type", "validated": true, "ani": 83.4345, "matched_fragments": 907, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella hinzii", "strain": "strain=NCTC13199", "accession": "GCA_900637615.1", "taxid": 103855, "species_taxid": 103855, "relation_to_type": "type", "validated": true, "ani": 83.4184, "matched_fragments": 928, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella hinzii", "strain": "strain=LMG 13501", "accession": "GCA_001548475.1", "taxid": 103855, "species_taxid": 103855, "relation_to_type": "type", "validated": true, "ani": 83.408, "matched_fragments": 905, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Bordetella bronchiseptica", "strain": "strain=CCUG 219", "accession": "GCA_021391275.1", "taxid": 518, "species_taxid": 518, "relation_to_type": "suspected-type", "validated": true, "ani": 80.5851, "matched_fragments": 586, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter xylosoxidans", "strain": "strain=PartM-Axylosoxidans-RM8376", "accession": "GCA_022870085.1", "taxid": 85698, "species_taxid": 85698, "relation_to_type": "type", "validated": true, "ani": 80.053, "matched_fragments": 611, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter insolitus", "strain": "strain=NCTC 13520", "accession": "GCA_024168865.1", "taxid": 217204, "species_taxid": 217204, "relation_to_type": "type", "validated": true, "ani": 79.4752, "matched_fragments": 586, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Castellaniella defragrans", "strain": "strain=DSM 12141", "accession": "GCA_014203015.1", "taxid": 75697, "species_taxid": 75697, "relation_to_type": "type", "validated": true, "ani": 77.9643, "matched_fragments": 264, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Hydrogenophaga aromaticivorans", "strain": "strain=D2P1", "accession": "GCA_013387465.1", "taxid": 2610898, "species_taxid": 2610898, "relation_to_type": "type", "validated": true, "ani": 77.0572, "matched_fragments": 150, "total_fragments": 1257, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_000612485.1", "gtdb_species": "s__Bordetella holmesii", "ani": 99.9816, "matched_fragments": 1229, "total_fragments": 1257, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.94", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 92, "status": "conclusive" }, { "accession": "GCF_002261355.1", "gtdb_species": "s__Bordetella sp002261355", "ani": 85.1554, "matched_fragments": 996, "total_fragments": 1257, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella", "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_000657795.2", 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"coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 1.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Bordetella", "holmesii" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }