{ "type": "genome", "identifier": "GCF_003063245.1", "organism": "Arcobacter caeni", "title": "Arcobacter caeni", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Universitat Rovira i Virgili", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003063245.1", "bioproject": "PRJNA224116", "biosample": "SAMN06286566", "wgs_master": "MUXE00000000.1", "refseq_category": "reference genome", "taxid": "1912877", "species_taxid": "1912877", "organism_name": "Arcobacter caeni", "infraspecific_name": "strain=RW17-10", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/04/23", "asm_name": "ASM306324v1", "asm_submitter": "Universitat Rovira i Virgili", "gbrs_paired_asm": "GCA_003063245.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/063/245/GCF_003063245.1_ASM306324v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2415164", "genome_size_ungapped": "2415164", "gc_percent": "27.000000", "replicon_count": "0", "scaffold_count": "59", "contig_count": "59", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003063245.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "2428", "protein_coding_gene_count": "2359", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-04-23", "dateModified": "2018-04-23", "datePublished": "2018-04-23", "_annotation": { "sample_count": 1, "sample_organism": [ "Arcobacter caeni" ], "sample_taxid": [ "1912877" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Spain" ], "sample_host_location_id": [], "data_size": "0.650 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)": "2415164", "Number of Sequences": "59", "Longest Sequences (bp)": "299802", "N50 (bp)": "123111", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "27.1", "Number of CDSs": "2359", "Average Protein Length": "318.6", "Coding Ratio (%)": "93.4", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Arcobacter caeni", "strain": "strain=RW17-10", "accession": "GCA_003063245.1", "taxid": 1912877, "species_taxid": 1912877, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 779, "total_fragments": 779, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Arcobacter suis", "strain": "strain=CECT7833", "accession": "GCA_004023465.1", "taxid": 1278212, "species_taxid": 1278212, "relation_to_type": "type", "validated": true, "ani": 88.2201, "matched_fragments": 617, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter suis", "strain": "strain=CECT 7833", "accession": "GCA_003544815.1", "taxid": 1278212, "species_taxid": 1278212, "relation_to_type": "type", "validated": true, "ani": 88.1781, "matched_fragments": 637, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter venerupis", "strain": "strain=CECT7836", "accession": "GCA_004023405.1", "taxid": 1054033, "species_taxid": 1054033, "relation_to_type": "type", "validated": true, "ani": 86.5159, "matched_fragments": 597, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter venerupis", "strain": "strain=LMG 26156", "accession": "GCA_013201665.1", "taxid": 1054033, "species_taxid": 1054033, "relation_to_type": "type", "validated": true, "ani": 86.4639, "matched_fragments": 615, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter ellisii", "strain": "strain=LMG 26155", "accession": "GCA_003544915.1", "taxid": 913109, "species_taxid": 913109, "relation_to_type": "type", "validated": true, "ani": 83.9581, "matched_fragments": 590, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter ellisii", "strain": "strain=CECT 7837", "accession": "GCA_004115815.1", "taxid": 913109, "species_taxid": 913109, "relation_to_type": "type", "validated": true, "ani": 83.9556, "matched_fragments": 565, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter cloacae", "strain": "strain=CECT 7834", "accession": "GCA_004115805.1", "taxid": 1054034, "species_taxid": 1054034, "relation_to_type": "type", "validated": true, "ani": 83.8917, "matched_fragments": 546, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Arcobacter cloacae", "strain": "strain=LMG 26153", "accession": "GCA_013201935.1", "taxid": 1054034, "species_taxid": 1054034, "relation_to_type": "type", "validated": true, "ani": 83.8879, "matched_fragments": 559, "total_fragments": 779, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003063245.1", "gtdb_species": "s__Aliarcobacter caeni", "ani": 100.0, "matched_fragments": 779, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "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": "conclusive" }, { "accession": "GCF_003544815.1", "gtdb_species": "s__Aliarcobacter suis", "ani": 88.1181, "matched_fragments": 640, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013201665.1", "gtdb_species": "s__Aliarcobacter venerupis", "ani": 86.4404, "matched_fragments": 617, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "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": "GCA_017995775.1", "gtdb_species": "s__Aliarcobacter sp017995775", "ani": 86.0672, "matched_fragments": 497, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "99.13", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_018816105.1", "gtdb_species": "s__Aliarcobacter sp018816105", "ani": 84.2327, "matched_fragments": 517, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "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_013177675.1", "gtdb_species": "s__Aliarcobacter acticola", "ani": 83.9713, "matched_fragments": 565, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "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_003544915.1", "gtdb_species": "s__Aliarcobacter ellisii", "ani": 83.914, "matched_fragments": 593, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.73", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.92", 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"0.88", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_013177635.1", "gtdb_species": "s__Aliarcobacter aquimarinus", "ani": 83.5045, "matched_fragments": 555, "total_fragments": 779, "gtdb_taxonomy": "d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.531, "cell_length": 0.145, "doubling_h": 0.086, "growth_tmp": 30.545, "optimum_tmp": 28.45, "optimum_ph": 7.25, "genome_size": 2607833.553, "gc_content": 27.345, "coding_genes": 2595.468, "rRNA16S_genes": 4.5, "tRNA_genes": 56.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.916, "range_salinity": 1.0, "facultative_respiration": 0.0, "anaerobic_respiration": 0.062, "aerobic_respiration": 0.937, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.666, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.222, "spiral_cell_shape": 0.111 }, "_genome_taxon": [ "Arcobacter", "caeni" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }