{ "type": "genome", "identifier": "GCF_002021985.1", "organism": "Campylobacter pinnipediorum subsp. caledonicus", "title": "Campylobacter pinnipediorum subsp. caledonicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA, ARS, WRRC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002021985.1", "bioproject": "PRJNA224116", "biosample": "SAMN03737985", "wgs_master": "na", "refseq_category": "na", "taxid": "1874362", "species_taxid": "1965231", "organism_name": "Campylobacter pinnipediorum subsp. caledonicus", "infraspecific_name": "strain=M302/10/6", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/03/06", "asm_name": "ASM202198v1", "asm_submitter": "USDA, ARS, WRRC", "gbrs_paired_asm": "GCA_002021985.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/021/985/GCF_002021985.1_ASM202198v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1705426", "genome_size_ungapped": "1705426", "gc_percent": "30.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-03-05", "total_gene_count": "1732", "protein_coding_gene_count": "1658", "non_coding_gene_count": "57", "pubmed_id": "28629508" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-03-06", "dateModified": "2017-03-06", "datePublished": "2017-03-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Campylobacter pinnipediorum subsp. caledonicus" ], "sample_taxid": [ "1874362" ], "sample_host_organism": [ "seal" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom: Scotland" ], "sample_host_location_id": [], "data_size": "0.462 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)": "1705426", "Number of Sequences": "1", "Longest Sequences (bp)": "1705426", "N50 (bp)": "1705426", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "30.4", "Number of CDSs": "1682", "Average Protein Length": "309.4", "Coding Ratio (%)": "91.6", "Number of rRNAs": "6", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter mucosalis", "strain": "strain=ATCC 43264", "accession": "GCA_013372205.1", "taxid": 202, "species_taxid": 202, "relation_to_type": "type", "validated": true, "ani": 77.9818, "matched_fragments": 126, "total_fragments": 568, "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": 77.8801, "matched_fragments": 102, "total_fragments": 568, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter avium", "strain": "strain=LMG 24591", "accession": "GCA_002238335.1", "taxid": 522485, "species_taxid": 522485, "relation_to_type": "type", "validated": true, "ani": 77.6495, "matched_fragments": 52, "total_fragments": 568, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter mucosalis", "strain": "strain=ATCC 43264", "accession": "GCA_012978755.1", "taxid": 202, "species_taxid": 202, "relation_to_type": "type", "validated": true, "ani": 77.4812, "matched_fragments": 120, "total_fragments": 568, "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": 77.3544, "matched_fragments": 71, "total_fragments": 568, "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": 77.333, "matched_fragments": 118, "total_fragments": 568, "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": 77.2364, "matched_fragments": 95, "total_fragments": 568, "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": 77.1385, "matched_fragments": 121, "total_fragments": 568, "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": 76.9503, "matched_fragments": 115, "total_fragments": 568, "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": 76.3815, "matched_fragments": 58, "total_fragments": 568, "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": 76.3631, "matched_fragments": 63, "total_fragments": 568, "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": 76.2854, "matched_fragments": 89, "total_fragments": 568, "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": 76.2251, "matched_fragments": 85, "total_fragments": 568, "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": 76.1758, "matched_fragments": 93, "total_fragments": 568, "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": 76.164, "matched_fragments": 55, "total_fragments": 568, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halarcobacter ebronensis", "strain": "strain=LMG 27922", "accession": "GCA_013201825.1", "taxid": 1462615, "species_taxid": 1462615, "relation_to_type": "type", "validated": true, "ani": 76.1527, "matched_fragments": 51, "total_fragments": 568, "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": 76.1306, "matched_fragments": 65, "total_fragments": 568, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002022005.1", "gtdb_species": "s__Campylobacter_A caledonicus", "ani": 99.2605, "matched_fragments": 554, "total_fragments": 568, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.31", "min_intra_species_ani": "99.26", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.97", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_002021925.1", "gtdb_species": "s__Campylobacter_A pinnipediorum", "ani": 94.8027, "matched_fragments": 515, "total_fragments": 568, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.45", "min_intra_species_ani": "97.81", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.95", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_004803835.1", "gtdb_species": "s__Campylobacter_A sp004803835", "ani": 78.1959, "matched_fragments": 126, "total_fragments": 568, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.48", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_013372205.1", "gtdb_species": 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"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", "pinnipediorum", "subsp.", "caledonicus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }