{ "type": "genome", "identifier": "GCF_000254135.1", "organism": "Campylobacter coli LMG 9860", "title": "Campylobacter coli LMG 9860", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Cornell University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000254135.1", "bioproject": "PRJNA224116", "biosample": "SAMN02428959", "wgs_master": "AINS00000000.1", "refseq_category": "na", "taxid": "887308", "species_taxid": "195", "organism_name": "Campylobacter coli LMG 9860", "infraspecific_name": "strain=LMG 9860", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2012/03/16", "asm_name": "ASM25413v2", "asm_submitter": "Cornell University", "gbrs_paired_asm": "GCA_000254135.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/254/135/GCF_000254135.1_ASM25413v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1851478", "genome_size_ungapped": "1851478", "gc_percent": "31.000000", "replicon_count": "0", "scaffold_count": "187", "contig_count": "187", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000254135.1-RS_2024_03_20", "annotation_date": "2024-03-20", "total_gene_count": "2051", "protein_coding_gene_count": "1926", "non_coding_gene_count": "35", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2012-03-16", "dateModified": "2012-03-16", "datePublished": "2012-03-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter coli LMG 9860" ], "sample_taxid": [ "887308" ], "sample_host_organism": [ "Homo sapiens" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada" ], "sample_host_location_id": [], "data_size": "0.513 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)": "1851478", "Number of Sequences": "187", "Longest Sequences (bp)": "125993", "N50 (bp)": "42746", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "31.0", "Number of CDSs": "1888", "Average Protein Length": "292.7", "Coding Ratio (%)": "89.5", "Number of rRNAs": "2", "Number of tRNAs": "29", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter coli", "strain": "strain=LMG 9860", "accession": "GCA_000254135.2", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 544, "total_fragments": 548, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter coli", "strain": "strain=LMG6440", "accession": "GCA_003590975.1", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 99.9967, "matched_fragments": 548, "total_fragments": 548, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter coli", "strain": "strain=CCUG 11283", "accession": "GCA_008802085.1", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 99.9966, "matched_fragments": 548, "total_fragments": 548, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter coli", "strain": "strain=NCTC11366", "accession": "GCA_900446355.1", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 99.9932, "matched_fragments": 548, "total_fragments": 548, "ani_threshold": 95, "status": "conclusive" }, { "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": 85.6118, "matched_fragments": 422, "total_fragments": 548, "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": 81.4361, "matched_fragments": 381, "total_fragments": 548, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter taeniopygiae", "strain": "strain=MIT10-5678", "accession": "GCA_005406225.1", "taxid": 2510188, "species_taxid": 2510188, "relation_to_type": "type", "validated": true, "ani": 81.003, "matched_fragments": 345, "total_fragments": 548, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter aviculae", "strain": "strain=MIT17-670", "accession": "GCA_005406215.1", "taxid": 2510190, "species_taxid": 2510190, "relation_to_type": "type", "validated": true, "ani": 80.9688, "matched_fragments": 358, "total_fragments": 548, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000254135.1", "gtdb_species": "s__Campylobacter_D coli", "ani": 100.0, "matched_fragments": 544, "total_fragments": 548, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.69", "min_intra_species_ani": "96.32", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.84", "num_clustered_genomes": 983, "status": "conclusive" }, { "accession": "GCF_001492295.1", "gtdb_species": "s__Campylobacter_D coli_B", "ani": 93.7063, "matched_fragments": 496, "total_fragments": 548, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.33", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.85", "num_clustered_genomes": 59, "status": "-" }, { "accession": "GCF_000470055.1", "gtdb_species": "s__Campylobacter_D coli_A", "ani": 92.2293, "matched_fragments": 457, "total_fragments": 548, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.85", "min_intra_species_ani": "97.41", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.91", "num_clustered_genomes": 86, "status": "-" }, { "accession": "GCF_001457695.1", "gtdb_species": "s__Campylobacter_D jejuni", "ani": 85.5665, "matched_fragments": 427, "total_fragments": 548, "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": "GCA_000163995.1", "gtdb_species": "s__Campylobacter_D jejuni_A", "ani": 84.1133, "matched_fragments": 427, "total_fragments": 548, "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": "GCF_002179165.1", "gtdb_species": "s__Campylobacter_D jejuni_B", "ani": 83.868, "matched_fragments": 411, "total_fragments": 548, "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": "GCF_001687475.2", "gtdb_species": "s__Campylobacter_D hepaticus", "ani": 81.4546, "matched_fragments": 380, "total_fragments": 548, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.94", "min_intra_species_ani": "99.56", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.97", "num_clustered_genomes": 33, "status": "-" }, { "accession": "GCF_004378855.1", "gtdb_species": "s__Campylobacter_D sp004378855", "ani": 81.3224, "matched_fragments": 312, "total_fragments": 548, "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": "GCF_005406215.1", "gtdb_species": "s__Campylobacter_D aviculae", "ani": 80.9809, "matched_fragments": 358, "total_fragments": 548, "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": "GCF_005406205.1", "gtdb_species": "s__Campylobacter_D estrildidarum", "ani": 80.9662, "matched_fragments": 340, "total_fragments": 548, "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": "GCF_016598935.1", "gtdb_species": "s__Campylobacter_D sp016598935", "ani": 80.7029, "matched_fragments": 335, "total_fragments": 548, "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": -0.699, "cell_length": -0.699, "doubling_h": 0.058, "growth_tmp": 37.0, "optimum_tmp": 41.722, "optimum_ph": 7.0, "genome_size": 1719161.597, "gc_content": 30.971, "coding_genes": 1799.438, "rRNA16S_genes": 2.818, "tRNA_genes": 43.167, "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": 0.0, "thermophilic_range_tmp": 1.0, "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", "coli", "LMG", "9860" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }