{ "type": "genome", "identifier": "GCF_003660265.1", "organism": "Helicobacter mehlei", "title": "Helicobacter mehlei", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbiology and Parasitology VF UL, Slovenia", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003660265.1", "bioproject": "PRJNA224116", "biosample": "SAMN09989576", "wgs_master": "QXQP00000000.1", "refseq_category": "na", "taxid": "2316080", "species_taxid": "2316080", "organism_name": "Helicobacter mehlei", "infraspecific_name": "strain=L15", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/10/15", "asm_name": "ASM366026v1", "asm_submitter": "Institute of Microbiology and Parasitology VF UL, Slovenia", "gbrs_paired_asm": "GCA_003660265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/660/265/GCF_003660265.1_ASM366026v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1647349", "genome_size_ungapped": "1647349", "gc_percent": "46.000000", "replicon_count": "0", "scaffold_count": "102", "contig_count": "102", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-01-29", "total_gene_count": "1682", "protein_coding_gene_count": "1566", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-10-15", "dateModified": "2018-10-15", "datePublished": "2018-10-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Helicobacter mehlei" ], "sample_taxid": [ "2316080" ], "sample_host_organism": [ "Vulpes vulpes" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.467 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "1647349", "Number of Sequences": "102", "Longest Sequences (bp)": "147999", "N50 (bp)": "61423", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "45.8", "Number of CDSs": "1568", "Average Protein Length": "310.9", "Coding Ratio (%)": "88.8", "Number of rRNAs": "3", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Helicobacter mehlei", "strain": "strain=L15", "accession": "GCA_003660265.1", "taxid": 2316080, "species_taxid": 2316080, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 510, "total_fragments": 510, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Helicobacter bizzozeronii", "strain": "strain=CIP 105233", "accession": "GCA_017979515.1", "taxid": 56877, "species_taxid": 56877, "relation_to_type": "type", "validated": true, "ani": 90.7249, "matched_fragments": 406, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter vulpis", "strain": "strain=L2", "accession": "GCA_003660395.1", "taxid": 2316076, "species_taxid": 2316076, "relation_to_type": "type", "validated": true, "ani": 81.2381, "matched_fragments": 252, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter labacensis", "strain": "strain=L9", "accession": "GCA_003660285.1", "taxid": 2316079, "species_taxid": 2316079, "relation_to_type": "type", "validated": true, "ani": 79.5193, "matched_fragments": 242, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter felis", "strain": "strain=ATCC 49179", "accession": "GCA_000200595.1", "taxid": 214, "species_taxid": 214, "relation_to_type": "type", "validated": true, "ani": 79.3251, "matched_fragments": 220, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter ailurogastricus", "strain": "", "accession": "GCA_001282945.1", "taxid": 1578720, "species_taxid": 1578720, "relation_to_type": "type", "validated": true, "ani": 79.3153, "matched_fragments": 205, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter salomonis", "strain": "strain=CIP 105607", "accession": "GCA_017979425.1", "taxid": 56878, "species_taxid": 56878, "relation_to_type": "type", "validated": true, "ani": 79.0013, "matched_fragments": 176, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter heilmannii", "strain": "", "accession": "GCA_001283065.1", "taxid": 35817, "species_taxid": 35817, "relation_to_type": "type", "validated": true, "ani": 78.6384, "matched_fragments": 197, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter heilmannii", "strain": "strain=LMG 26292", "accession": "GCA_017979395.1", "taxid": 35817, "species_taxid": 35817, "relation_to_type": "type", "validated": true, "ani": 78.5882, "matched_fragments": 186, "total_fragments": 510, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003660265.1", "gtdb_species": "s__Helicobacter_E mehlei", "ani": 100.0, "matched_fragments": 510, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.56", "min_intra_species_ani": "99.56", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_000263275.1", "gtdb_species": "s__Helicobacter_E bizzozeronii", "ani": 90.7937, "matched_fragments": 428, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.96", "min_intra_species_ani": "95.19", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_003660395.1", "gtdb_species": "s__Helicobacter_E vulpis", "ani": 81.2392, "matched_fragments": 252, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "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_003660285.1", "gtdb_species": "s__Helicobacter_E labacensis", "ani": 79.438, "matched_fragments": 246, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900197855.1", "gtdb_species": "s__Helicobacter_E cynogastricus", "ani": 79.3877, "matched_fragments": 192, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "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_000200595.1", "gtdb_species": "s__Helicobacter_E felis", "ani": 79.3109, "matched_fragments": 222, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.57", "min_intra_species_ani": "97.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_001282945.1", "gtdb_species": "s__Helicobacter_E ailurogastricus", "ani": 79.2916, "matched_fragments": 206, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.41", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_001283065.1", "gtdb_species": "s__Helicobacter_E heilmannii", "ani": 78.6813, "matched_fragments": 195, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.65", "min_intra_species_ani": "98.18", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 9, "status": "-" }, { "accession": "GCF_902196135.1", "gtdb_species": "s__Helicobacter_E suis_A", "ani": 77.308, "matched_fragments": 159, "total_fragments": 510, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_E", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.68", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "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", "mehlei" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }