{ "type": "genome", "identifier": "GCF_005406225.1", "organism": "Campylobacter taeniopygiae", "title": "Campylobacter taeniopygiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "MIT", "publication": [ {} ], "properties": { "assembly_accession": "GCF_005406225.1", "bioproject": "PRJNA224116", "biosample": "SAMN07710583", "wgs_master": "NXLY00000000.1", "refseq_category": "reference genome", "taxid": "2510188", "species_taxid": "2510188", "organism_name": "Campylobacter taeniopygiae", "infraspecific_name": "strain=MIT10-5678", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/05/15", "asm_name": "ASM540622v1", "asm_submitter": "MIT", "gbrs_paired_asm": "GCA_005406225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/005/406/225/GCF_005406225.1_ASM540622v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1725278", "genome_size_ungapped": "1725278", "gc_percent": "29.500000", "replicon_count": "0", "scaffold_count": "88", "contig_count": "88", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_005406225.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "1831", "protein_coding_gene_count": "1721", "non_coding_gene_count": "47", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-05-15", "dateModified": "2019-05-15", "datePublished": "2019-05-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter taeniopygiae" ], "sample_taxid": [ "2510188" ], "sample_host_organism": [ "Taeniopygia guttata" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA" ], "sample_host_location_id": [], "data_size": "0.469 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)": "1725278", "Number of Sequences": "88", "Longest Sequences (bp)": "190204", "N50 (bp)": "99681", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "29.4", "Number of CDSs": "1702", "Average Protein Length": "305.9", "Coding Ratio (%)": "90.5", "Number of rRNAs": "1", "Number of tRNAs": "40", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter taeniopygiae", "strain": "strain=MIT10-5678", "accession": "GCA_005406225.1", "taxid": 2510188, "species_taxid": 2510188, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 544, "total_fragments": 545, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter aviculae", "strain": "strain=MIT17-670", "accession": "GCA_005406215.1", "taxid": 2510190, "species_taxid": 2510190, "relation_to_type": "type", "validated": true, "ani": 89.4853, "matched_fragments": 444, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter jejuni", "strain": "strain=NCTC11351", "accession": "GCA_001457695.1", "taxid": 197, "species_taxid": 197, "relation_to_type": "type", "validated": true, "ani": 81.2031, "matched_fragments": 372, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter jejuni subsp. jejuni", "strain": "strain=CCUG 11284", "accession": "GCA_008802045.1", "taxid": 32022, "species_taxid": 197, "relation_to_type": "type", "validated": true, "ani": 81.1785, "matched_fragments": 367, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter jejuni subsp. jejuni", "strain": "strain=ATCC 33560", "accession": "GCA_000254515.2", "taxid": 32022, "species_taxid": 197, "relation_to_type": "type", "validated": true, "ani": 81.107, "matched_fragments": 330, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter coli", "strain": "strain=LMG 9860", "accession": "GCA_000254135.2", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 81.0705, "matched_fragments": 346, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter coli", "strain": "strain=LMG6440", "accession": "GCA_003590975.1", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 81.0037, "matched_fragments": 369, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter coli", "strain": "strain=CCUG 11283", "accession": "GCA_008802085.1", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 80.9805, "matched_fragments": 367, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hepaticus", "strain": "strain=HV10", "accession": "GCA_001687475.2", "taxid": 1813019, "species_taxid": 1813019, "relation_to_type": "type", "validated": true, "ani": 80.0436, "matched_fragments": 318, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter novaezeelandiae", "strain": "strain=B423b", "accession": "GCA_004323845.1", "taxid": 2267891, "species_taxid": 2267891, "relation_to_type": "type", "validated": true, "ani": 79.2889, "matched_fragments": 281, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter cuniculorum", "strain": "strain=LMG 24588", "accession": "GCA_002104335.1", "taxid": 374106, "species_taxid": 374106, "relation_to_type": "type", "validated": true, "ani": 78.7246, "matched_fragments": 253, "total_fragments": 545, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_005406225.1", "gtdb_species": "s__Campylobacter_D taeniopygiae", "ani": 100.0, "matched_fragments": 544, "total_fragments": 545, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_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": "conclusive" }, { "accession": "GCF_016598935.1", "gtdb_species": "s__Campylobacter_D sp016598935", "ani": 90.3677, "matched_fragments": 425, "total_fragments": 545, "gtdb_taxonomy": 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"d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_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_001457695.1", "gtdb_species": "s__Campylobacter_D jejuni", "ani": 81.1671, "matched_fragments": 375, "total_fragments": 545, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.50", "min_intra_species_ani": "95.69", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.84", "num_clustered_genomes": 1918, "status": "-" }, { "accession": "GCF_002179165.1", "gtdb_species": "s__Campylobacter_D jejuni_B", "ani": 80.9344, "matched_fragments": 367, "total_fragments": 545, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_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": -0.396, "cell_length": 0.155, "doubling_h": 0.058, "growth_tmp": 37.939, "optimum_tmp": 38.124, "optimum_ph": 6.461, "genome_size": 1793418.147, "gc_content": 33.91, "coding_genes": 1694.451, "rRNA16S_genes": 2.877, "tRNA_genes": 42.86, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.869, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.178, "aerobic_respiration": 0.821, "mesophilic_range_tmp": 0.888, "thermophilic_range_tmp": 0.111, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.35, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.05, "vibrio_cell_shape": 0.1, "spiral_cell_shape": 0.5 }, "_genome_taxon": [ "Campylobacter", "taeniopygiae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }