{ "type": "genome", "identifier": "GCF_013372125.1", "organism": "Campylobacter curvus", "title": "Campylobacter curvus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA, ARS, WRRC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013372125.1", "bioproject": "PRJNA224116", "biosample": "SAMN14886871", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "200", "species_taxid": "200", "organism_name": "Campylobacter curvus", "infraspecific_name": "strain=ATCC 35224", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/24", "asm_name": "ASM1337212v1", "asm_submitter": "USDA, ARS, WRRC", "gbrs_paired_asm": "GCA_013372125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/372/125/GCF_013372125.1_ASM1337212v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1974918", "genome_size_ungapped": "1974918", "gc_percent": "44.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013372125.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "1982", "protein_coding_gene_count": "1895", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-24", "dateModified": "2020-06-24", "datePublished": "2020-06-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter curvus" ], "sample_taxid": [ "200" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Massachusetts" ], "sample_host_location_id": [], "data_size": "0.550 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)": "1974918", "Number of Sequences": "1", "Longest Sequences (bp)": "1974918", "N50 (bp)": "1974918", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "44.3", "Number of CDSs": "1924", "Average Protein Length": "310.7", "Coding Ratio (%)": "90.8", "Number of rRNAs": "6", "Number of tRNAs": "46", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter curvus", "strain": "strain=ATCC 35224", "accession": "GCA_013372125.1", "taxid": 200, "species_taxid": 200, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 657, "total_fragments": 658, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter curvus", "strain": "strain=FDAARGOS_1547", "accession": "GCA_020736225.1", "taxid": 200, "species_taxid": 200, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9987, "matched_fragments": 656, "total_fragments": 658, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter curvus", "strain": "strain=DSM 6644", "accession": "GCA_000376325.1", "taxid": 200, "species_taxid": 200, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9828, "matched_fragments": 648, "total_fragments": 658, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter curvus", "strain": "strain=ATCC 35224", "accession": "GCA_012978875.1", "taxid": 200, "species_taxid": 200, "relation_to_type": "suspected-type", "validated": true, "ani": 99.9785, "matched_fragments": 636, "total_fragments": 658, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter massiliensis", "strain": "strain=Marseille-Q3452", "accession": "GCA_014253065.1", "taxid": 2762557, "species_taxid": 2762557, "relation_to_type": "type", "validated": true, "ani": 78.6776, "matched_fragments": 253, "total_fragments": 658, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter showae", "strain": "strain=ATCC 51146", "accession": "GCA_004803815.1", "taxid": 204, "species_taxid": 204, "relation_to_type": "suspected-type", "validated": true, "ani": 78.5816, "matched_fragments": 253, "total_fragments": 658, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter concisus", "strain": "strain=ATCC 33237", "accession": "GCA_001298465.1", "taxid": 199, "species_taxid": 199, "relation_to_type": "suspected-type", "validated": true, "ani": 78.4774, "matched_fragments": 242, "total_fragments": 658, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013372125.1", "gtdb_species": "s__Campylobacter_A curvus", "ani": 100.0, "matched_fragments": 657, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.39", "min_intra_species_ani": "95.49", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 16, "status": "conclusive" }, { "accession": "GCF_900699785.1", "gtdb_species": "s__Campylobacter_A showae_D", "ani": 78.7713, "matched_fragments": 242, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "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": 3, "status": "-" }, { "accession": "GCF_014253065.1", "gtdb_species": "s__Campylobacter_A sp014253065", "ani": 78.7587, "matched_fragments": 257, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "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_900573985.1", "gtdb_species": "s__Campylobacter_A showae_E", "ani": 78.5895, "matched_fragments": 260, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "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_004803815.1", "gtdb_species": "s__Campylobacter_A showae", "ani": 78.5858, "matched_fragments": 251, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003048375.1", "gtdb_species": "s__Campylobacter_A concisus_T", "ani": 78.5788, "matched_fragments": 282, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.30", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.85", "num_clustered_genomes": 33, "status": "-" }, { "accession": "GCF_003048835.2", "gtdb_species": "s__Campylobacter_A concisus_D", "ani": 78.5588, "matched_fragments": 279, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0092, "mean_intra_species_ani": "97.26", "min_intra_species_ani": "95.33", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_015230015.1", "gtdb_species": "s__Campylobacter_A concisus_AF", "ani": 78.4997, "matched_fragments": 269, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "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_000344295.2", "gtdb_species": "s__Campylobacter_A showae_B", "ani": 78.4775, "matched_fragments": 213, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "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_003048405.1", "gtdb_species": "s__Campylobacter_A concisus_Q", "ani": 78.4516, "matched_fragments": 249, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.74", "min_intra_species_ani": "96.49", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000466685.1", "gtdb_species": "s__Campylobacter_A concisus_A", "ani": 78.4293, "matched_fragments": 287, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.29", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_902460415.1", "gtdb_species": "s__Campylobacter_A concisus_Y", "ani": 78.4263, "matched_fragments": 233, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.32", "min_intra_species_ani": "95.32", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000313615.1", "gtdb_species": "s__Campylobacter_A showae_A", "ani": 78.4151, "matched_fragments": 236, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.64", "min_intra_species_ani": "96.14", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_002913225.1", "gtdb_species": "s__Campylobacter_A concisus_J", "ani": 78.3971, "matched_fragments": 280, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.08", "min_intra_species_ani": "95.08", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_004803795.1", "gtdb_species": "s__Campylobacter_A rectus", "ani": 78.3521, "matched_fragments": 229, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "96.44", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.96", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003048675.2", "gtdb_species": "s__Campylobacter_A concisus_F", "ani": 78.3341, "matched_fragments": 296, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0092, "mean_intra_species_ani": "95.49", "min_intra_species_ani": "95.08", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.88", "num_clustered_genomes": 22, "status": "-" }, { "accession": "GCF_002912895.1", "gtdb_species": "s__Campylobacter_A concisus_G", "ani": 78.2821, "matched_fragments": 230, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.40", "min_intra_species_ani": "95.36", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.89", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_018375265.1", "gtdb_species": "s__Campylobacter_A concisus_AB", "ani": 78.2165, "matched_fragments": 167, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.35", "min_intra_species_ani": "95.14", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.77", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_018145735.1", "gtdb_species": "s__Campylobacter_A sp018145735", "ani": 77.5365, "matched_fragments": 154, "total_fragments": 658, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "99.05", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.96", "num_clustered_genomes": 3, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.301, "doubling_h": 0.058, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.0, "genome_size": 1966592.286, "gc_content": 44.433, "coding_genes": 1887.0, "rRNA16S_genes": 3.0, "tRNA_genes": 46.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "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": [ "Campylobacter", "curvus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }