{ "type": "genome", "identifier": "GCF_016806695.1", "organism": "Campylobacter bilis", "title": "Campylobacter bilis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "RMIT University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_016806695.1", "bioproject": "PRJNA224116", "biosample": "SAMN13671134", "wgs_master": "WUED00000000.1", "refseq_category": "na", "taxid": "2691918", "species_taxid": "2691918", "organism_name": "Campylobacter bilis", "infraspecific_name": "strain=VicNov18", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/02/03", "asm_name": "ASM1680669v1", "asm_submitter": "RMIT University", "gbrs_paired_asm": "GCA_016806695.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/016/806/695/GCF_016806695.1_ASM1680669v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1447069", "genome_size_ungapped": "1447069", "gc_percent": "30.500000", "replicon_count": "0", "scaffold_count": "41", "contig_count": "41", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_016806695.1-RS_2024_05_17", "annotation_date": "2024-05-17", "total_gene_count": "1537", "protein_coding_gene_count": "1393", "non_coding_gene_count": "49", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-02-03", "dateModified": "2021-02-03", "datePublished": "2021-02-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter bilis" ], "sample_taxid": [ "2691918" ], "sample_host_organism": [ "chicken" ], "sample_host_organism_id": [], "sample_host_disease": [ "spotty liver disease" ], "sample_host_disease_id": [], "sample_host_location": [ "Australia: Euroa, Victoria" ], "sample_host_location_id": [], "data_size": "0.395 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)": "1447069", "Number of Sequences": "41", "Longest Sequences (bp)": "148444", "N50 (bp)": "107626", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "30.7", "Number of CDSs": "1478", "Average Protein Length": "296.5", "Coding Ratio (%)": "90.8", "Number of rRNAs": "2", "Number of tRNAs": "41", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter bilis", "strain": "strain=VicNov18", "accession": "GCA_016806695.1", "taxid": 2691918, "species_taxid": 2691918, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 460, "total_fragments": 464, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Campylobacter hepaticus", "strain": "strain=HV10", "accession": "GCA_001687475.2", "taxid": 1813019, "species_taxid": 1813019, "relation_to_type": "type", "validated": true, "ani": 85.2693, "matched_fragments": 423, "total_fragments": 464, "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": 83.9465, "matched_fragments": 361, "total_fragments": 464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter jejuni subsp. jejuni", "strain": "strain=type strain: CCUG11284", "accession": "GCA_905410075.1", "taxid": 32022, "species_taxid": 197, "relation_to_type": "type", "validated": true, "ani": 83.7849, "matched_fragments": 398, "total_fragments": 464, "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": 83.7266, "matched_fragments": 403, "total_fragments": 464, "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": 83.7227, "matched_fragments": 403, "total_fragments": 464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter lari subsp. concheus", "strain": "strain=LMG 21009", "accession": "GCA_008245025.1", "taxid": 488545, "species_taxid": 201, "relation_to_type": "type", "validated": true, "ani": 77.9803, "matched_fragments": 201, "total_fragments": 464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter upsaliensis", "strain": "strain=FDAARGOS_1518", "accession": "GCA_020297605.1", "taxid": 28080, "species_taxid": 28080, "relation_to_type": "type", "validated": true, "ani": 77.8685, "matched_fragments": 179, "total_fragments": 464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter upsaliensis", "strain": "strain=NCTC11541", "accession": "GCA_900637395.1", "taxid": 28080, "species_taxid": 28080, "relation_to_type": "type", "validated": true, "ani": 77.8151, "matched_fragments": 182, "total_fragments": 464, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter upsaliensis", "strain": "strain=DSM 5365", "accession": "GCA_000620965.1", "taxid": 28080, "species_taxid": 28080, "relation_to_type": "type", "validated": true, "ani": 77.5141, "matched_fragments": 183, "total_fragments": 464, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009362725.1", "gtdb_species": "s__Campylobacter_D hepaticus_A", "ani": 100.0, "matched_fragments": 460, "total_fragments": 464, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001687475.2", "gtdb_species": "s__Campylobacter_D hepaticus", "ani": 85.2693, "matched_fragments": 423, "total_fragments": 464, "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_001457695.1", "gtdb_species": "s__Campylobacter_D jejuni", "ani": 83.7227, "matched_fragments": 403, "total_fragments": 464, "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": 83.6432, "matched_fragments": 383, "total_fragments": 464, "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_014305285.1", "gtdb_species": "s__Campylobacter_D jejuni_D", "ani": 83.5671, "matched_fragments": 388, "total_fragments": 464, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_002179165.1", "gtdb_species": "s__Campylobacter_D jejuni_B", "ani": 81.1287, "matched_fragments": 338, "total_fragments": 464, "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_016599045.1", "gtdb_species": "s__Campylobacter_D sp016599045", "ani": 79.1666, "matched_fragments": 256, "total_fragments": 464, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "98.98", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_008245025.1", "gtdb_species": "s__Campylobacter_D concheus", "ani": 77.9803, "matched_fragments": 201, "total_fragments": 464, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.27", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_900637395.1", "gtdb_species": "s__Campylobacter_D upsaliensis", "ani": 77.8697, "matched_fragments": 179, "total_fragments": 464, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.80", "min_intra_species_ani": "95.96", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.88", "num_clustered_genomes": 18, "status": "-" }, { "accession": "GCF_002238335.1", "gtdb_species": "s__Campylobacter_D avium", "ani": 76.841, "matched_fragments": 91, "total_fragments": 464, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.95", "min_intra_species_ani": "99.95", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "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", "bilis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }