{ "type": "genome", "identifier": "GCF_004323845.1", "organism": "Campylobacter novaezeelandiae", "title": "Campylobacter novaezeelandiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Massey University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004323845.1", "bioproject": "PRJNA224116", "biosample": "SAMN09629882", "wgs_master": "QPGR00000000.1", "refseq_category": "na", "taxid": "2267891", "species_taxid": "2267891", "organism_name": "Campylobacter novaezeelandiae", "infraspecific_name": "strain=B423b", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/04", "asm_name": "ASM432384v1", "asm_submitter": "Massey University", "gbrs_paired_asm": "GCA_004323845.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/323/845/GCF_004323845.1_ASM432384v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1571819", "genome_size_ungapped": "1571819", "gc_percent": "27.500000", "replicon_count": "0", "scaffold_count": "59", "contig_count": "59", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004323845.1-RS_2024_08_04", "annotation_date": "2024-08-04", "total_gene_count": "1663", "protein_coding_gene_count": "1569", "non_coding_gene_count": "45", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-04", "dateModified": "2019-03-04", "datePublished": "2019-03-04", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter novaezeelandiae" ], "sample_taxid": [ "2267891" ], "sample_host_organism": [ "Anas platyrhynchos" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "New Zealand" ], "sample_host_location_id": [], "data_size": "0.424 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)": "1571819", "Number of Sequences": "59", "Longest Sequences (bp)": "253485", "N50 (bp)": "119547", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.4", "Number of CDSs": "1569", "Average Protein Length": "305.5", "Coding Ratio (%)": "91.5", "Number of rRNAs": "2", "Number of tRNAs": "39", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter novaezeelandiae", "strain": "strain=B423b", "accession": "GCA_004323845.1", "taxid": 2267891, "species_taxid": 2267891, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 501, "total_fragments": 504, "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": 80.232, "matched_fragments": 305, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter coli", "strain": "strain=CCUG 11283", "accession": "GCA_008802085.1", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 80.107, "matched_fragments": 317, "total_fragments": 504, "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": 79.952, "matched_fragments": 278, "total_fragments": 504, "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": 79.9142, "matched_fragments": 303, "total_fragments": 504, "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": 79.9035, "matched_fragments": 298, "total_fragments": 504, "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": 79.8881, "matched_fragments": 301, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter coli", "strain": "strain=LMG 9860", "accession": "GCA_000254135.2", "taxid": 195, "species_taxid": 195, "relation_to_type": "type", "validated": true, "ani": 79.7614, "matched_fragments": 284, "total_fragments": 504, "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": 79.5051, "matched_fragments": 287, "total_fragments": 504, "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": 79.4752, "matched_fragments": 286, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter bilis", "strain": "strain=VicNov18", "accession": "GCA_016806695.1", "taxid": 2691918, "species_taxid": 2691918, "relation_to_type": "type", "validated": true, "ani": 78.9366, "matched_fragments": 243, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter ornithocola", "strain": "strain=WBE38", "accession": "GCA_001705345.1", "taxid": 1848766, "species_taxid": 1848766, "relation_to_type": "type", "validated": true, "ani": 78.6868, "matched_fragments": 201, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter lari", "strain": "strain=FDAARGOS_1101", "accession": "GCA_016726265.1", "taxid": 201, "species_taxid": 201, "relation_to_type": "type", "validated": true, "ani": 78.6626, "matched_fragments": 210, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter ornithocola", "strain": "strain=LMG 29815", "accession": "GCA_013201605.1", "taxid": 1848766, "species_taxid": 1848766, "relation_to_type": "type", "validated": true, "ani": 78.6478, "matched_fragments": 209, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter lari subsp. lari", "strain": "strain=LMG 8846", "accession": "GCA_013372185.1", "taxid": 650054, "species_taxid": 201, "relation_to_type": "type", "validated": true, "ani": 78.6417, "matched_fragments": 209, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter lari", "strain": "strain=NCTC11352", "accession": "GCA_900446615.1", "taxid": 201, "species_taxid": 201, "relation_to_type": "type", "validated": true, "ani": 78.601, "matched_fragments": 210, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter volucris", "strain": "strain=CCUG 57498", "accession": "GCA_008801985.1", "taxid": 1031542, "species_taxid": 1031542, "relation_to_type": "type", "validated": true, "ani": 78.4679, "matched_fragments": 230, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter lari subsp. lari", "strain": "strain=ATCC 35221", "accession": "GCA_900111465.1", "taxid": 650054, "species_taxid": 201, "relation_to_type": "type", "validated": true, "ani": 78.4656, "matched_fragments": 199, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter volucris", "strain": "strain=LMG 24380", "accession": "GCA_008245045.1", "taxid": 1031542, "species_taxid": 1031542, "relation_to_type": "type", "validated": true, "ani": 78.4604, "matched_fragments": 229, "total_fragments": 504, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004323845.1", "gtdb_species": "s__Campylobacter_D novaezeelandiae", "ani": 100.0, "matched_fragments": 501, "total_fragments": 504, "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": "98.04", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "conclusive" }, { "accession": "GCF_016599045.1", "gtdb_species": "s__Campylobacter_D sp016599045", "ani": 90.1168, "matched_fragments": 444, "total_fragments": 504, "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_001457695.1", "gtdb_species": "s__Campylobacter_D jejuni", "ani": 79.8943, "matched_fragments": 305, "total_fragments": 504, "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": 79.8777, "matched_fragments": 289, "total_fragments": 504, "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_000254135.1", "gtdb_species": "s__Campylobacter_D coli", "ani": 79.8001, "matched_fragments": 282, "total_fragments": 504, "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": "-" }, { "accession": "GCF_016598935.1", "gtdb_species": "s__Campylobacter_D sp016598935", "ani": 79.6143, "matched_fragments": 286, "total_fragments": 504, "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": 79.5868, "matched_fragments": 285, "total_fragments": 504, "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_001687475.2", "gtdb_species": "s__Campylobacter_D hepaticus", "ani": 79.5051, "matched_fragments": 287, "total_fragments": 504, "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_005406215.1", "gtdb_species": "s__Campylobacter_D aviculae", "ani": 79.4752, "matched_fragments": 286, "total_fragments": 504, "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_001492295.1", "gtdb_species": "s__Campylobacter_D coli_B", "ani": 79.35, "matched_fragments": 286, "total_fragments": 504, "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_009362725.1", "gtdb_species": "s__Campylobacter_D hepaticus_A", "ani": 78.9659, "matched_fragments": 241, "total_fragments": 504, "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": "-" }, { "accession": "GCF_004378855.1", "gtdb_species": "s__Campylobacter_D sp004378855", "ani": 78.9386, "matched_fragments": 247, "total_fragments": 504, "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_013201605.1", "gtdb_species": "s__Campylobacter_D ornithocola", "ani": 78.7075, "matched_fragments": 206, "total_fragments": 504, "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": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013372185.1", "gtdb_species": "s__Campylobacter_D lari", "ani": 78.6417, "matched_fragments": 209, "total_fragments": 504, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 13, "status": "-" }, { "accession": "GCF_008245045.1", "gtdb_species": "s__Campylobacter_D volucris", "ani": 78.4845, "matched_fragments": 227, "total_fragments": 504, "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": "97.46", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.86", "num_clustered_genomes": 15, "status": "-" }, { "accession": "GCF_004357905.1", "gtdb_species": "s__Campylobacter_D lari_D", "ani": 78.4826, "matched_fragments": 206, "total_fragments": 504, "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": -0.396, "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", "novaezeelandiae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }