{ "type": "genome", "identifier": "GCF_000762845.2", "organism": "Helicobacter japonicus", "title": "Helicobacter japonicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Massachusetts Institute of Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000762845.2", "bioproject": "PRJNA224116", "biosample": "SAMN03074667", "wgs_master": "JRMQ00000000.2", "refseq_category": "na", "taxid": "425400", "species_taxid": "425400", "organism_name": "Helicobacter japonicus", "infraspecific_name": "strain=MIT 01-6451", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/05/22", "asm_name": "ASM76284v2", "asm_submitter": "Massachusetts Institute of Technology", "gbrs_paired_asm": "GCA_000762845.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/845/GCF_000762845.2_ASM76284v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1945265", "genome_size_ungapped": "1945265", "gc_percent": "35.500000", "replicon_count": "0", "scaffold_count": "49", "contig_count": "49", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000762845.2-RS_2024_04_03", "annotation_date": "2024-04-03", "total_gene_count": "1996", "protein_coding_gene_count": "1909", "non_coding_gene_count": "43", "pubmed_id": "25428971" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-05-22", "dateModified": "2019-05-22", "datePublished": "2019-05-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Helicobacter japonicus" ], "sample_taxid": [ "425400" ], "sample_host_organism": [ "mouse" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], 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"total_fragments": 626, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Helicobacter labetoulli", "strain": "strain=48519", "accession": "GCA_003670275.1", "taxid": 2315333, "species_taxid": 2315333, "relation_to_type": "type", "validated": true, "ani": 78.6494, "matched_fragments": 272, "total_fragments": 626, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter cinaedi", "strain": "strain=ATCC BAA-847", "accession": "GCA_000349975.1", "taxid": 213, "species_taxid": 213, "relation_to_type": "type", "validated": true, "ani": 78.6179, "matched_fragments": 297, "total_fragments": 626, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter cinaedi", "strain": "strain=CCUG 18818", "accession": "GCA_000155475.1", "taxid": 213, "species_taxid": 213, "relation_to_type": "type", "validated": true, "ani": 78.5769, "matched_fragments": 286, "total_fragments": 626, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter cinaedi", "strain": "strain=CCUG 18818", "accession": "GCA_003215615.1", "taxid": 213, "species_taxid": 213, "relation_to_type": "type", "validated": true, "ani": 78.4525, "matched_fragments": 282, "total_fragments": 626, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter marmotae", "strain": "strain=MIT 98-6070", "accession": "GCA_003364255.1", "taxid": 152490, "species_taxid": 152490, "relation_to_type": "type", "validated": true, "ani": 78.0931, "matched_fragments": 281, "total_fragments": 626, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter jaachi", "strain": "strain=MIT 09-6949", "accession": "GCA_000763135.2", "taxid": 1677920, "species_taxid": 1677920, "relation_to_type": "type", "validated": true, "ani": 77.6921, "matched_fragments": 219, "total_fragments": 626, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Helicobacter valdiviensis", "strain": "strain=WBE14", "accession": "GCA_003245365.1", "taxid": 1458358, "species_taxid": 1458358, "relation_to_type": "type", "validated": true, "ani": 77.1879, "matched_fragments": 52, "total_fragments": 626, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000762845.2", "gtdb_species": "s__Helicobacter_C japonicus", "ani": 100.0, "matched_fragments": 624, "total_fragments": 626, "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": "conclusive" }, { "accession": "GCF_000007905.1", "gtdb_species": "s__Helicobacter_C hepaticus", "ani": 83.2, "matched_fragments": 418, 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"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": "-" } ] }, "_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", "japonicus" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }