{ "type": "genome", "identifier": "GCF_000158455.1", "organism": "Helicobacter winghamensis ATCC BAA-430", "title": "Helicobacter winghamensis ATCC BAA-430", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Broad Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000158455.1", "bioproject": "PRJNA224116", "biosample": "SAMN02463715", "wgs_master": "ACDO00000000.1", "refseq_category": "na", "taxid": "556267", "species_taxid": "157268", "organism_name": "Helicobacter winghamensis ATCC BAA-430", "infraspecific_name": "strain=ATCC BAA-430", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2009/03/10", "asm_name": "ASM15845v1", "asm_submitter": "Broad Institute", "gbrs_paired_asm": "GCA_000158455.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/158/455/GCF_000158455.1_ASM15845v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1690216", "genome_size_ungapped": "1654865", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "21", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000158455.1-RS_2024_05_15", "annotation_date": "2024-05-15", "total_gene_count": "1735", "protein_coding_gene_count": "1666", "non_coding_gene_count": "43", "pubmed_id": "25212613" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2009-03-10", "dateModified": "2009-03-10", "datePublished": "2009-03-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Helicobacter winghamensis ATCC BAA-430" ], "sample_taxid": [ "556267" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not determined" ], "sample_host_location_id": [], "data_size": "0.456 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)": "1690216", "Number of Sequences": "21", "Longest Sequences (bp)": "655865", "N50 (bp)": "583100", "Gap Ratio (%)": "2.091508", "GCcontent (%)": "35.5", "Number of CDSs": "1651", "Average Protein Length": "308.1", "Coding Ratio (%)": "90.3", "Number of rRNAs": "2", "Number of tRNAs": "37", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Helicobacter winghamensis", "strain": "strain=ATCC BAA-430", "accession": "GCA_000158455.1", "taxid": 157268, "species_taxid": 157268, "relation_to_type": "type", "validated": true, "ani": 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"below_threshold" }, { "organism_name": "Helicobacter canadensis", "strain": "strain=MIT 98-5491", "accession": "GCA_000162575.1", "taxid": 123841, "species_taxid": 123841, "relation_to_type": "type", "validated": true, "ani": 77.9867, "matched_fragments": 189, "total_fragments": 555, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000158455.1", "gtdb_species": "s__Helicobacter_D winghamensis", "ani": 99.9996, "matched_fragments": 552, "total_fragments": 555, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.73", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_000765695.2", 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"s__Helicobacter_D sp003288905", "ani": 78.1719, "matched_fragments": 178, "total_fragments": 555, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D", "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_003245365.1", "gtdb_species": "s__Helicobacter_D valdiviensis", "ani": 78.1425, "matched_fragments": 186, "total_fragments": 555, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter_D", "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_000765675.1", "gtdb_species": "s__Helicobacter_D 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"filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 1.0 }, "_genome_taxon": [ "Helicobacter", "winghamensis", "ATCC", "BAA-430" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }