{ "type": "genome", "identifier": "GCF_003364205.1", "organism": "Helicobacter brantae", "title": "Helicobacter brantae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "MIT", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003364205.1", "bioproject": "PRJNA224116", "biosample": "SAMN07710586", "wgs_master": "NXLV00000000.1", "refseq_category": "reference genome", "taxid": "375927", "species_taxid": "375927", "organism_name": "Helicobacter brantae", "infraspecific_name": "strain=MIT 04-9366", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/07", "asm_name": "ASM336420v1", "asm_submitter": "MIT", "gbrs_paired_asm": "GCA_003364205.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/364/205/GCF_003364205.1_ASM336420v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1730760", "genome_size_ungapped": "1730760", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "37", "contig_count": "37", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003364205.1-RS_2024_05_04", "annotation_date": "2024-05-04", "total_gene_count": "1640", "protein_coding_gene_count": "1593", "non_coding_gene_count": "43", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-08-07", "dateModified": "2018-08-07", "datePublished": "2018-08-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Helicobacter brantae" ], "sample_taxid": [ "375927" ], "sample_host_organism": [ "Branta canadensis" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.474 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)": "1730760", "Number of Sequences": "37", "Longest Sequences (bp)": "267984", "N50 (bp)": "133474", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.1", "Number of CDSs": "1546", "Average Protein Length": "328.2", "Coding Ratio (%)": "87.9", "Number of rRNAs": "2", "Number of tRNAs": "37", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Helicobacter brantae", "strain": "strain=MIT 04-9366", "accession": "GCA_003364205.1", "taxid": 375927, "species_taxid": 375927, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 561, "total_fragments": 562, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Helicobacter cholecystus", "strain": "strain=ATCC 700242", "accession": "GCA_003364215.1", "taxid": 45498, "species_taxid": 45498, "relation_to_type": "type", "validated": true, "ani": 78.8443, "matched_fragments": 203, "total_fragments": 562, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter pametensis", "strain": "strain=ATCC 51478", "accession": "GCA_000518225.1", "taxid": 95149, "species_taxid": 95149, "relation_to_type": "type", "validated": true, "ani": 77.6748, "matched_fragments": 154, "total_fragments": 562, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter kayseriensis", "strain": "strain=faydin-H23", "accession": "GCA_021300655.1", "taxid": 2905877, "species_taxid": 2905877, "relation_to_type": "type", "validated": true, "ani": 77.5549, "matched_fragments": 126, "total_fragments": 562, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter enhydrae", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "conclusive" }, { "accession": "GCA_019115525.1", "gtdb_species": "s__Helicobacter_G avistercoris", "ani": 81.4002, "matched_fragments": 287, "total_fragments": 562, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_G", "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_003364215.1", "gtdb_species": "s__Helicobacter_G cholecystus", "ani": 78.8434, "matched_fragments": 203, "total_fragments": 562, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_G", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000155475.1", "gtdb_species": "s__Helicobacter_C cinaedi", "ani": 76.482, "matched_fragments": 61, "total_fragments": 562, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "98.84", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.91", "num_clustered_genomes": 38, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.358, "cell_length": 0.409, "doubling_h": 0.5, "growth_tmp": 37.166, "optimum_tmp": 36.65, "optimum_ph": 7.262, "genome_size": 1931302.958, "gc_content": 37.515, "coding_genes": 1769.479, "rRNA16S_genes": 1.895, "tRNA_genes": 37.181, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Helicobacter", "brantae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }