{ "type": "genome", "identifier": "GCF_013201685.1", "organism": "Campylobacter geochelonis", "title": "Campylobacter geochelonis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA, ARS, WRRC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013201685.1", "bioproject": "PRJNA224116", "biosample": "SAMN10884420", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1780362", "species_taxid": "1780362", "organism_name": "Campylobacter geochelonis", "infraspecific_name": "strain=LMG 29375", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/06/01", "asm_name": "ASM1320168v1", "asm_submitter": "USDA, ARS, WRRC", "gbrs_paired_asm": "GCA_013201685.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/201/685/GCF_013201685.1_ASM1320168v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2167961", "genome_size_ungapped": "2167961", "gc_percent": "33.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013201685.1-RS_2024_07_19", "annotation_date": "2024-07-19", "total_gene_count": "1997", "protein_coding_gene_count": "1913", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-06-01", "dateModified": "2020-06-01", "datePublished": "2020-06-01", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter geochelonis" ], "sample_taxid": [ "1780362" ], "sample_host_organism": [ "Testudo hermanni hermanni" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Italy" ], "sample_host_location_id": [], "data_size": "0.585 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)": "2167961", "Number of Sequences": "1", "Longest Sequences (bp)": "2167961", "N50 (bp)": "2167961", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "33.5", "Number of CDSs": "1966", "Average Protein Length": "312.9", "Coding Ratio (%)": "85.1", "Number of rRNAs": "6", "Number of tRNAs": "45", "Number of CRISPRs": "6" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter geochelonis", "strain": "strain=LMG 29375", "accession": "GCA_013201685.1", "taxid": 1780362, "species_taxid": 1780362, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 717, "total_fragments": 722, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter geochelonis", "strain": "strain=RC20", "accession": "GCA_900063025.1", "taxid": 1780362, "species_taxid": 1780362, "relation_to_type": "type", "validated": true, "ani": 99.9261, "matched_fragments": 679, "total_fragments": 722, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter iguaniorum", "strain": "strain=1485E", "accession": "GCA_000736415.1", "taxid": 1244531, "species_taxid": 1244531, "relation_to_type": "type", "validated": true, "ani": 78.0227, "matched_fragments": 119, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis subsp. lawsonii", "strain": "strain=CHY5", "accession": "GCA_013372165.1", "taxid": 91353, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 77.7131, "matched_fragments": 111, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.6606, "matched_fragments": 99, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter massiliensis", "strain": "strain=Marseille-Q3452", "accession": "GCA_014253065.1", "taxid": 2762557, "species_taxid": 2762557, "relation_to_type": "type", "validated": true, "ani": 77.5952, "matched_fragments": 57, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.5713, "matched_fragments": 97, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter blaseri", "strain": "strain=LMG 30333", "accession": "GCA_013201895.1", "taxid": 2042961, "species_taxid": 2042961, "relation_to_type": "type", "validated": true, "ani": 77.5184, "matched_fragments": 167, "total_fragments": 722, "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": 77.298, "matched_fragments": 98, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter corcagiensis", "strain": "strain=LMG 27932", "accession": "GCA_013201645.1", "taxid": 1448857, "species_taxid": 1448857, "relation_to_type": "type", "validated": true, "ani": 77.2821, "matched_fragments": 165, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter blaseri", "strain": "strain=17S00004-5", "accession": "GCA_003015205.1", "taxid": 2042961, "species_taxid": 2042961, "relation_to_type": "type", "validated": true, "ani": 77.2207, "matched_fragments": 163, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.1887, "matched_fragments": 98, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter corcagiensis", "strain": "strain=CIT 045", "accession": "GCA_000597805.1", "taxid": 1448857, "species_taxid": 1448857, "relation_to_type": "type", "validated": true, "ani": 76.9527, "matched_fragments": 161, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter portucalensis", "strain": "strain=FMV-PI01", "accession": "GCA_009690845.1", "taxid": 2608384, "species_taxid": 2608384, "relation_to_type": "type", "validated": true, "ani": 76.8737, "matched_fragments": 160, "total_fragments": 722, "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": 76.7834, "matched_fragments": 101, "total_fragments": 722, "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": 76.7126, "matched_fragments": 105, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter anatolicus", "strain": "strain=faydin-G140", "accession": "GCA_018145655.1", "taxid": 2829105, "species_taxid": 2829105, "relation_to_type": "type", "validated": true, "ani": 76.35, "matched_fragments": 102, "total_fragments": 722, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_013201685.1", "gtdb_species": "s__Campylobacter_B geochelonis", "ani": 100.0, "matched_fragments": 718, "total_fragments": 722, "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": "conclusive" }, { "accession": "GCF_000736415.1", "gtdb_species": "s__Campylobacter iguaniorum", "ani": 78.192, "matched_fragments": 119, "total_fragments": 722, "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_000413435.1", "gtdb_species": "s__Campylobacter_B ureolyticus_A", "ani": 77.5803, "matched_fragments": 162, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "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": "GCA_000495505.1", "gtdb_species": "s__Campylobacter testudinum", "ani": 77.5413, "matched_fragments": 115, "total_fragments": 722, "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_900475935.1", "gtdb_species": "s__Campylobacter fetus", "ani": 77.5125, "matched_fragments": 100, "total_fragments": 722, "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": "-" }, { "accession": "GCF_013201895.1", "gtdb_species": "s__Campylobacter_B blaseri", "ani": 77.4917, "matched_fragments": 169, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "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": 3, "status": "-" }, { "accession": "GCF_013372165.1", "gtdb_species": "s__Campylobacter lawsonii", "ani": 77.4346, "matched_fragments": 111, "total_fragments": 722, "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_003048835.2", "gtdb_species": "s__Campylobacter_A concisus_D", "ani": 77.3937, "matched_fragments": 95, "total_fragments": 722, "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_013201645.1", "gtdb_species": "s__Campylobacter_B corcagiensis", "ani": 77.3172, "matched_fragments": 163, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002912895.1", "gtdb_species": "s__Campylobacter_A concisus_G", "ani": 76.9884, "matched_fragments": 91, "total_fragments": 722, "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_012728225.1", "gtdb_species": "s__Campylobacter_B sp012728225", "ani": 76.9831, "matched_fragments": 98, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "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_001891085.1", "gtdb_species": "s__Campylobacter_A concisus_O", "ani": 76.9449, "matched_fragments": 95, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.13", "min_intra_species_ani": "95.13", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_012519705.1", "gtdb_species": "s__Campylobacter_B sp012519705", "ani": 76.8857, "matched_fragments": 164, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "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_009690845.1", "gtdb_species": "s__Campylobacter_B portucalensis", "ani": 76.8704, "matched_fragments": 161, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "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_003048535.1", "gtdb_species": "s__Campylobacter_A concisus_S", "ani": 76.8329, "matched_fragments": 96, "total_fragments": 722, "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": "GCA_017469645.1", "gtdb_species": "s__Campylobacter_B sp017469645", "ani": 76.808, "matched_fragments": 128, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_B", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.68", "min_intra_species_ani": "95.54", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.81", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_005406205.1", "gtdb_species": "s__Campylobacter_D estrildidarum", "ani": 76.3308, "matched_fragments": 51, "total_fragments": 722, "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": "-" }, { "accession": "GCA_017646085.1", "gtdb_species": "s__Campylobacter sp017646085", "ani": 76.1814, "matched_fragments": 64, "total_fragments": 722, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter", "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", "geochelonis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }