{ "type": "genome", "identifier": "GCF_002021925.1", "organism": "Campylobacter pinnipediorum subsp. pinnipediorum", "title": "Campylobacter pinnipediorum subsp. pinnipediorum", "description": "na", "data type": "Genome sequencing and assembly", "organization": "USDA, ARS, WRRC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002021925.1", "bioproject": "PRJNA224116", "biosample": "SAMN03737982", "wgs_master": "na", "refseq_category": "na", "taxid": "1660067", "species_taxid": "1965231", "organism_name": "Campylobacter pinnipediorum subsp. pinnipediorum", "infraspecific_name": "strain=RM17260", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/03/06", "asm_name": "ASM202192v1", "asm_submitter": "USDA, ARS, WRRC", "gbrs_paired_asm": "GCA_002021925.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/021/925/GCF_002021925.1_ASM202192v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "1782665", "genome_size_ungapped": "1782665", "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": "1850", "protein_coding_gene_count": "1778", "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. pinnipediorum" ], "sample_taxid": [ "1660067" ], "sample_host_organism": [ "Sea lion" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: California" ], "sample_host_location_id": [], "data_size": "0.484 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)": "1782665", "Number of Sequences": "1", "Longest Sequences (bp)": "1782665", "N50 (bp)": "1782665", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "30.4", "Number of CDSs": "1805", "Average Protein Length": "299.2", "Coding Ratio (%)": "90.9", "Number of rRNAs": "6", "Number of tRNAs": "45", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Campylobacter blaseri", "strain": "strain=LMG 30333", "accession": "GCA_013201895.1", "taxid": 2042961, "species_taxid": 2042961, "relation_to_type": "type", "validated": true, "ani": 78.6657, "matched_fragments": 140, "total_fragments": 594, "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": 78.4368, "matched_fragments": 137, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter mucosalis", "strain": "strain=ATCC 43264", "accession": "GCA_013372205.1", "taxid": 202, "species_taxid": 202, "relation_to_type": "type", "validated": true, "ani": 78.0754, "matched_fragments": 123, "total_fragments": 594, "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": 77.9914, "matched_fragments": 68, "total_fragments": 594, "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": 77.8516, "matched_fragments": 97, "total_fragments": 594, "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": 77.7615, "matched_fragments": 68, "total_fragments": 594, "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": 77.5742, "matched_fragments": 69, "total_fragments": 594, "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": 77.5428, "matched_fragments": 117, "total_fragments": 594, "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": 77.4598, "matched_fragments": 117, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter peloridis", "strain": "strain=LMG 23910", "accession": "GCA_000816785.1", "taxid": 488546, "species_taxid": 488546, "relation_to_type": "type", "validated": true, "ani": 77.3124, "matched_fragments": 81, "total_fragments": 594, "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": 77.269, "matched_fragments": 93, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis subsp. hyointestinalis", "strain": "strain=CCUG 14169", "accession": "GCA_013372145.1", "taxid": 91352, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 77.231, "matched_fragments": 78, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis", "strain": "strain=NCTC11608", "accession": "GCA_900460765.1", "taxid": 198, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 77.1953, "matched_fragments": 79, "total_fragments": 594, "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": 76.9364, "matched_fragments": 62, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis subsp. hyointestinalis", "strain": "strain=DSM 19053", "accession": "GCA_000705275.1", "taxid": 91352, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 76.6039, "matched_fragments": 74, "total_fragments": 594, "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": 76.5026, "matched_fragments": 63, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Campylobacter hyointestinalis", "strain": "strain=ATCC 35217", "accession": "GCA_900116585.1", "taxid": 198, "species_taxid": 198, "relation_to_type": "type", "validated": true, "ani": 76.4041, "matched_fragments": 78, "total_fragments": 594, "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": 76.3495, "matched_fragments": 89, "total_fragments": 594, "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": 76.1734, "matched_fragments": 84, "total_fragments": 594, "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": 75.859, "matched_fragments": 68, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halarcobacter ebronensis", "strain": "strain=CECT 8441", "accession": "GCA_004116565.1", "taxid": 1462615, "species_taxid": 1462615, "relation_to_type": "type", "validated": true, "ani": 75.0698, "matched_fragments": 61, "total_fragments": 594, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002021925.1", "gtdb_species": "s__Campylobacter_A pinnipediorum", "ani": 100.0, "matched_fragments": 593, "total_fragments": 594, "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": "conclusive" }, { "accession": "GCF_002022005.1", "gtdb_species": "s__Campylobacter_A caledonicus", "ani": 94.704, "matched_fragments": 536, "total_fragments": 594, "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": "-" }, { "accession": "GCF_013201895.1", "gtdb_species": "s__Campylobacter_B blaseri", "ani": 78.6839, "matched_fragments": 140, "total_fragments": 594, "gtdb_taxonomy": 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"coccobacillus_cell_shape": 0.05, "vibrio_cell_shape": 0.1, "spiral_cell_shape": 0.5 }, "_genome_taxon": [ "Campylobacter", "pinnipediorum", "subsp.", "pinnipediorum" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }