{ "type": "genome", "identifier": "GCF_021300615.1", "organism": "Helicobacter anatolicus", "title": "Helicobacter anatolicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Erciyes Univ. Faculty of Veterinary Medicine", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021300615.1", "bioproject": "PRJNA224116", "biosample": "SAMN24291161", "wgs_master": "JAJTMY000000000.1", "refseq_category": "reference genome", "taxid": "2905874", "species_taxid": "2905874", "organism_name": "Helicobacter anatolicus", "infraspecific_name": "strain=faydin-H8", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/12/27", "asm_name": "ASM2130061v1", "asm_submitter": "Erciyes Univ. Faculty of Veterinary Medicine", "gbrs_paired_asm": "GCA_021300615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/300/615/GCF_021300615.1_ASM2130061v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1512511", "genome_size_ungapped": "1512511", "gc_percent": "32.000000", "replicon_count": "0", "scaffold_count": "12", "contig_count": "12", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021300615.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "1475", "protein_coding_gene_count": "1418", "non_coding_gene_count": "43", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-12-27", "dateModified": "2021-12-27", "datePublished": "2021-12-27", "_annotation": { "sample_count": 1, "sample_organism": [ "Helicobacter anatolicus" ], "sample_taxid": [ "2905874" ], "sample_host_organism": [ "Crow" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Turkey:Kayseri" ], "sample_host_location_id": [], "data_size": "0.414 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)": "1512511", "Number of Sequences": "12", "Longest Sequences (bp)": "544299", "N50 (bp)": "346110", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "32.0", "Number of CDSs": "1417", "Average Protein Length": "325.6", "Coding Ratio (%)": "91.5", "Number of rRNAs": "2", "Number of tRNAs": "37", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Helicobacter anatolicus", "strain": "strain=faydin-H8", "accession": "GCA_021300615.1", "taxid": 2905874, "species_taxid": 2905874, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 497, "total_fragments": 497, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Helicobacter anseris", "strain": "strain=MIT 04-9362", "accession": "GCA_003364335.1", "taxid": 375926, "species_taxid": 375926, "relation_to_type": "type", "validated": true, "ani": 78.0234, "matched_fragments": 164, "total_fragments": 497, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter mustelae", "strain": "strain=NCTC12198", "accession": "GCA_900476215.1", "taxid": 217, "species_taxid": 217, "relation_to_type": "type", "validated": true, "ani": 77.492, "matched_fragments": 84, "total_fragments": 497, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter burdigaliensis", "strain": "strain=CNRCH 2005/566H", "accession": "GCA_003670295.1", "taxid": 2315334, "species_taxid": 2315334, "relation_to_type": "type", "validated": true, "ani": 77.132, "matched_fragments": 61, "total_fragments": 497, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter japonicus", "strain": "strain=MIT 01-6451", "accession": "GCA_000762845.2", "taxid": 425400, "species_taxid": 425400, "relation_to_type": "type", "validated": true, "ani": 77.0301, "matched_fragments": 54, "total_fragments": 497, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003364335.1", "gtdb_species": "s__Helicobacter_H anseris", "ani": 78.0234, "matched_fragments": 164, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H", "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_900199585.1", "gtdb_species": "s__Helicobacter_H sp900199585", "ani": 77.8659, "matched_fragments": 156, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004368235.1", "gtdb_species": "s__Helicobacter_H anseris_A", "ani": 77.5028, "matched_fragments": 106, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H", "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_900476215.1", "gtdb_species": "s__Helicobacter_H mustelae", "ani": 77.492, "matched_fragments": 84, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_H", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.73", "min_intra_species_ani": "99.46", "mean_intra_species_af": "1.00", "min_intra_species_af": "0.99", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002272895.1", "gtdb_species": "s__Helicobacter_J sp002272895", "ani": 77.2292, "matched_fragments": 70, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J", "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_000762845.2", "gtdb_species": "s__Helicobacter_C japonicus", "ani": 77.0301, "matched_fragments": 54, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900198655.1", "gtdb_species": "s__Helicobacter_F equorum_A", "ani": 76.8753, "matched_fragments": 57, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_F", "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_002272785.1", "gtdb_species": "s__Helicobacter_J sp002272785", "ani": 76.8733, "matched_fragments": 70, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J", "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_002272795.1", "gtdb_species": "s__Helicobacter_J sp002272795", "ani": 76.8349, "matched_fragments": 73, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J", "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_002272835.1", "gtdb_species": "s__Helicobacter_J sp002272835", "ani": 76.7917, "matched_fragments": 80, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_J", "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_000007905.1", "gtdb_species": "s__Helicobacter_C hepaticus", "ani": 76.2327, "matched_fragments": 57, "total_fragments": 497, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.74", "min_intra_species_ani": "98.74", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "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": 0.057, "aerobic_respiration": 0.942, "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", "anatolicus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }