{ "type": "genome", "identifier": "GCF_900445945.1", "organism": "Bordetella trematum", "title": "Bordetella trematum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "SC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900445945.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4504055", "wgs_master": "UFUJ00000000.1", "refseq_category": "reference genome", "taxid": "123899", "species_taxid": "123899", "organism_name": "Bordetella trematum", "infraspecific_name": "strain=NCTC12995", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/08", "asm_name": "52067_A01", "asm_submitter": "SC", "gbrs_paired_asm": "GCA_900445945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/445/945/GCF_900445945.1_52067_A01", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4498245", "genome_size_ungapped": "4498245", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900445945.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "4218", "protein_coding_gene_count": "4118", "non_coding_gene_count": "85", "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 trematum" ], "sample_taxid": [ "123899" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [ "not available: to be reported later" ], "sample_host_disease_id": [], "sample_host_location": [ "Germany" ], "sample_host_location_id": [], "data_size": "1.236 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)": "4498245", "Number of Sequences": "2", "Longest Sequences (bp)": "4476238", "N50 (bp)": "4476238", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.5", "Number of CDSs": "4168", "Average Protein Length": "326.5", "Coding Ratio (%)": "90.7", "Number of rRNAs": "12", "Number of tRNAs": "70", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Bordetella trematum", "strain": "strain=NCTC12995", "accession": "GCA_900445945.1", "taxid": 123899, "species_taxid": 123899, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1497, "total_fragments": 1499, "ani_threshold": 95, 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"GCA_020735925.1", "taxid": 519, "species_taxid": 519, "relation_to_type": "suspected-type", "validated": true, "ani": 81.5284, "matched_fragments": 780, "total_fragments": 1499, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Achromobacter insuavis", "strain": "strain=LMG 26845", "accession": "GCA_902859645.1", "taxid": 1287735, "species_taxid": 1287735, "relation_to_type": "type", "validated": true, "ani": 81.4247, "matched_fragments": 822, "total_fragments": 1499, "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": 81.271, "matched_fragments": 845, "total_fragments": 1499, "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": 80.4284, "matched_fragments": 740, "total_fragments": 1499, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pusillimonas minor", "strain": "strain=YC-7-48", "accession": "GCA_014237865.1", "taxid": 2697024, "species_taxid": 2697024, "relation_to_type": "type", "validated": true, "ani": 77.7453, "matched_fragments": 170, "total_fragments": 1499, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cupriavidus numazuensis", "strain": "strain=LMG 26411", "accession": "GCA_905397435.1", "taxid": 221992, "species_taxid": 221992, "relation_to_type": "type", "validated": true, "ani": 77.4684, "matched_fragments": 319, "total_fragments": 1499, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900078335.1", "gtdb_species": "s__Bordetella 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82.6619, "matched_fragments": 860, "total_fragments": 1499, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.54", "min_intra_species_ani": "99.31", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 26, "status": "-" }, { "accession": "GCF_002261355.1", "gtdb_species": "s__Bordetella sp002261355", "ani": 81.8627, "matched_fragments": 797, "total_fragments": 1499, "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_000306945.1", "gtdb_species": "s__Bordetella pertussis", "ani": 81.6688, "matched_fragments": 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