{ "type": "genome", "identifier": "GCF_008693125.1", "organism": "Campylobacter fetus subsp. fetus", "title": "Campylobacter fetus subsp. fetus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Gothenburg - CCUG", "publication": [ {} ], "properties": { "assembly_accession": "GCF_008693125.1", "bioproject": "PRJNA224116", "biosample": "SAMN12771118", "wgs_master": "VXKL00000000.1", "refseq_category": "na", "taxid": "32019", "species_taxid": "196", "organism_name": "Campylobacter fetus subsp. fetus", "infraspecific_name": "strain=CCUG 6823 AT", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/24", "asm_name": "ASM869312v1", "asm_submitter": "University of Gothenburg - CCUG", "gbrs_paired_asm": "GCA_008693125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/693/125/GCF_008693125.1_ASM869312v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1740377", "genome_size_ungapped": "1740377", "gc_percent": "33.000000", "replicon_count": "0", "scaffold_count": "29", "contig_count": "29", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_008693125.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "1803", "protein_coding_gene_count": "1722", "non_coding_gene_count": "48", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-24", "dateModified": "2019-09-24", "datePublished": "2019-09-24", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter fetus subsp. fetus" ], "sample_taxid": [ "32019" ], "sample_host_organism": [ "sheep" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom: London" ], "sample_host_location_id": [], "data_size": "0.482 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)": "1740377", "Number of Sequences": "29", "Longest Sequences (bp)": "367584", "N50 (bp)": "263025", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "33.2", "Number of CDSs": "1732", "Average Protein Length": "306.0", "Coding Ratio (%)": "91.4", "Number of rRNAs": "2", "Number of tRNAs": "42", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter fetus subsp. fetus", "strain": "strain=CCUG 6823 AT", "accession": "GCA_008693125.1", "taxid": 32019, "species_taxid": 196, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 564, "total_fragments": 566, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter fetus subsp. fetus", "strain": "strain=NCTC10842", "accession": "GCA_900475935.1", "taxid": 32019, "species_taxid": 196, "relation_to_type": "type", "validated": true, "ani": 99.9982, "matched_fragments": 566, "total_fragments": 566, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter fetus subsp. venerealis", "strain": "strain=NCTC 10354", "accession": "GCA_008271385.1", "taxid": 32020, "species_taxid": 196, "relation_to_type": "type", "validated": true, "ani": 99.4966, "matched_fragments": 558, "total_fragments": 566, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter hyointestinalis", "strain": "strain=NCTC11608", "accession": "GCA_900460765.1", "taxid": 198, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 82.4281, "matched_fragments": 352, "total_fragments": 566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis subsp. hyointestinalis", "strain": "strain=DSM 19053", "accession": "GCA_000705275.1", "taxid": 91352, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 82.378, "matched_fragments": 347, "total_fragments": 566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis subsp. lawsonii", "strain": "strain=CCUG 34538", "accession": "GCA_008802075.1", "taxid": 91353, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 81.545, "matched_fragments": 331, "total_fragments": 566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis subsp. lawsonii", "strain": "strain=CHY5", "accession": "GCA_003289475.1", "taxid": 91353, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 81.5198, "matched_fragments": 322, "total_fragments": 566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter iguaniorum", "strain": "strain=1485E", "accession": "GCA_000736415.1", "taxid": 1244531, "species_taxid": 1244531, "relation_to_type": "type", "validated": true, "ani": 78.9961, "matched_fragments": 268, "total_fragments": 566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter geochelonis", "strain": "strain=LMG 29375", "accession": "GCA_013201685.1", "taxid": 1780362, "species_taxid": 1780362, "relation_to_type": "type", "validated": true, "ani": 77.0144, "matched_fragments": 102, "total_fragments": 566, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter geochelonis", "strain": "strain=RC20", "accession": "GCA_900063025.1", "taxid": 1780362, "species_taxid": 1780362, "relation_to_type": "type", "validated": true, "ani": 76.966, "matched_fragments": 102, "total_fragments": 566, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900475935.1", "gtdb_species": "s__Campylobacter fetus", "ani": 99.9982, "matched_fragments": 566, "total_fragments": 566, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.49", "min_intra_species_ani": "97.66", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 71, "status": "conclusive" }, { "accession": "GCA_000495505.1", "gtdb_species": "s__Campylobacter testudinum", "ani": 92.0694, "matched_fragments": 537, "total_fragments": 566, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 37, "status": "-" }, { "accession": "GCF_013372145.1", "gtdb_species": "s__Campylobacter hyointestinalis", "ani": 82.4957, "matched_fragments": 348, "total_fragments": 566, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.64", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.88", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_013372165.1", "gtdb_species": "s__Campylobacter lawsonii", "ani": 81.6009, "matched_fragments": 332, "total_fragments": 566, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.50", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.87", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_000736415.1", "gtdb_species": "s__Campylobacter iguaniorum", "ani": 78.9967, "matched_fragments": 268, "total_fragments": 566, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "97.69", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_013201685.1", "gtdb_species": "s__Campylobacter_B geochelonis", "ani": 77.0152, "matched_fragments": 102, "total_fragments": 566, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.40", "min_intra_species_ani": "99.12", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 4, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.385, "cell_length": 0.155, "doubling_h": 0.058, "growth_tmp": 37.0, "optimum_tmp": 37.0, "optimum_ph": 7.0, "genome_size": 1857712.246, "gc_content": 33.355, "coding_genes": 1798.368, "rRNA16S_genes": 3.0, "tRNA_genes": 42.0, "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", "fetus", "subsp.", "fetus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }