{ "type": "genome", "identifier": "GCF_003364265.1", "organism": "Helicobacter aurati", "title": "Helicobacter aurati", "description": "na", "data type": "Genome sequencing and assembly", "organization": "MIT", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003364265.1", "bioproject": "PRJNA224116", "biosample": "SAMN07710585", "wgs_master": "NXLW00000000.1", "refseq_category": "reference genome", "taxid": "137778", "species_taxid": "137778", "organism_name": "Helicobacter aurati", "infraspecific_name": "strain=MIT 97-5075", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/08/07", "asm_name": "ASM336426v1", "asm_submitter": "MIT", "gbrs_paired_asm": "GCA_003364265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/364/265/GCF_003364265.1_ASM336426v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1973922", "genome_size_ungapped": "1973922", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "48", "contig_count": "48", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003364265.1-RS_2024_04_27", "annotation_date": "2024-04-27", "total_gene_count": "1851", "protein_coding_gene_count": "1774", "non_coding_gene_count": "42", "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 aurati" ], "sample_taxid": [ "137778" ], "sample_host_organism": [ "Mesocricetus auratus" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.555 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)": "1973922", "Number of Sequences": "48", "Longest Sequences (bp)": "269432", "N50 (bp)": "119626", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "35.3", "Number of CDSs": "1743", "Average Protein Length": "326.0", "Coding Ratio (%)": "86.4", "Number of rRNAs": "2", "Number of tRNAs": "36", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Helicobacter aurati", "strain": "strain=MIT 97-5075", "accession": "GCA_003364265.1", "taxid": 137778, "species_taxid": 137778, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 636, "total_fragments": 638, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Helicobacter muridarum", "strain": "strain=NCTC12714", "accession": "GCA_900450885.1", "taxid": 216, "species_taxid": 216, "relation_to_type": "type", "validated": true, "ani": 77.8915, "matched_fragments": 185, "total_fragments": 638, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter muridarum", "strain": "strain=ST1", "accession": "GCA_000765805.2", "taxid": 216, "species_taxid": 216, "relation_to_type": "type", "validated": true, "ani": 77.7412, "matched_fragments": 185, "total_fragments": 638, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter didelphidarum", "strain": "strain=MIT 17-337", "accession": "GCA_003364195.1", "taxid": 2040648, "species_taxid": 2040648, "relation_to_type": "type", "validated": true, "ani": 77.0818, "matched_fragments": 85, "total_fragments": 638, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter trogontum", "strain": "strain=ATCC 700114", "accession": "GCA_000765905.2", "taxid": 50960, "species_taxid": 50960, "relation_to_type": "type", "validated": true, "ani": 76.8828, "matched_fragments": 70, "total_fragments": 638, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter bilis", "strain": "strain=ATCC 51630", "accession": "GCA_000686565.1", "taxid": 37372, "species_taxid": 37372, "relation_to_type": "type", "validated": true, "ani": 76.8157, "matched_fragments": 77, "total_fragments": 638, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter bilis", "strain": "strain=ATCC 51630", "accession": "GCA_000765785.2", "taxid": 37372, "species_taxid": 37372, "relation_to_type": "type", "validated": true, "ani": 76.8147, "matched_fragments": 77, "total_fragments": 638, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003364265.1", "gtdb_species": "s__Helicobacter_A aurati", "ani": 100.0, "matched_fragments": 636, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_000765805.2", "gtdb_species": "s__Helicobacter_A muridarum", "ani": 77.7413, "matched_fragments": 185, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003364195.1", "gtdb_species": "s__Helicobacter_A didelphidarum", "ani": 77.1142, "matched_fragments": 84, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "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_000765905.2", "gtdb_species": "s__Helicobacter_A trogontum", "ani": 76.8828, "matched_fragments": 70, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.76", "min_intra_species_ani": "97.01", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_001999985.1", "gtdb_species": "s__Helicobacter_A bilis_A", "ani": 76.8255, "matched_fragments": 76, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "ani_circumscription_radius": 96.3516, "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_000686565.1", "gtdb_species": "s__Helicobacter_A bilis", "ani": 76.7872, "matched_fragments": 78, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "ani_circumscription_radius": 96.5798, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.91", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_900198625.1", "gtdb_species": "s__Helicobacter_A rappini", "ani": 76.7416, "matched_fragments": 76, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "ani_circumscription_radius": 96.5798, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "97.29", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900198365.1", "gtdb_species": "s__Helicobacter_A bilis_B", "ani": 76.5306, "matched_fragments": 79, "total_fragments": 638, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_A", "ani_circumscription_radius": 95.8327, "mean_intra_species_ani": "99.79", "min_intra_species_ani": "99.65", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.222, "cell_length": 0.602, "doubling_h": 0.5, "growth_tmp": 37.0, "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", "aurati" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }