{ "type": "genome", "identifier": "GCF_000401515.2", "organism": "Piscirickettsia salmonis LF-89 = ATCC VR-1361", "title": "Piscirickettsia salmonis LF-89 = ATCC VR-1361", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Texas at San Antonio", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000401515.2", "bioproject": "PRJNA224116", "biosample": "SAMN02471204", "wgs_master": "ASSK00000000.2", "refseq_category": "na", "taxid": "1227812", "species_taxid": "1238", "organism_name": "Piscirickettsia salmonis LF-89 = ATCC VR-1361", "infraspecific_name": "strain=LF-89", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/09/26", "asm_name": "ASM40151v2", "asm_submitter": "University of Texas at San Antonio", "gbrs_paired_asm": "GCA_000401515.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/401/515/GCF_000401515.2_ASM40151v2", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2805478", "genome_size_ungapped": "2805478", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "355", "contig_count": "355", "annotation_provider": "NCBI RefSeq", "annotation_name": "NCBI Prokaryotic Genome Annotation Pipeline (PGAP)", "annotation_date": "2024-02-03", "total_gene_count": "2944", "protein_coding_gene_count": "2725", "non_coding_gene_count": "58", "pubmed_id": "24201203" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-09-26", "dateModified": "2013-09-26", "datePublished": "2013-09-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Piscirickettsia salmonis LF-89 = ATCC VR-1361" ], "sample_taxid": [ "1227812" ], "sample_host_organism": [ "coho salmon" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Chile" ], "sample_host_location_id": [], "data_size": "0.794 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "2805478", "Number of Sequences": "355", "Longest Sequences (bp)": "59816", "N50 (bp)": "12340", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.6", "Number of CDSs": "2542", "Average Protein Length": "294.3", "Coding Ratio (%)": "80.0", "Number of rRNAs": "5", "Number of tRNAs": "47", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Piscirickettsia salmonis", "strain": "strain=LF-89", "accession": "GCA_000401515.2", "taxid": 1238, "species_taxid": 1238, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 732, "total_fragments": 740, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Piscirickettsia salmonis", "strain": "strain=LF-89", "accession": "GCA_000297215.2", "taxid": 1238, "species_taxid": 1238, "relation_to_type": "suspected-type", "validated": true, "ani": 99.8309, "matched_fragments": 708, "total_fragments": 740, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Piscirickettsia salmonis", "strain": "strain=ATCC VR-1361", "accession": "GCA_000300295.4", "taxid": 1238, "species_taxid": 1238, "relation_to_type": "suspected-type", "validated": true, "ani": 95.6006, "matched_fragments": 706, "total_fragments": 740, "ani_threshold": 95, "status": "conclusive" } ], "cc_result": { "completeness": 91.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000297215.2", "gtdb_species": "s__Piscirickettsia salmonis", "ani": 99.8428, "matched_fragments": 708, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Piscirickettsiales;f__Piscirickettsiaceae;g__Piscirickettsia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.52", "min_intra_species_ani": "95.10", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.81", "num_clustered_genomes": 87, "status": "conclusive" }, { "accession": "GCA_001644975.1", "gtdb_species": "s__Piscirickettsia sp001644975", "ani": 92.6607, "matched_fragments": 643, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Piscirickettsiales;f__Piscirickettsiaceae;g__Piscirickettsia", "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_001720395.1", "gtdb_species": "s__Piscirickettsia litoralis", "ani": 78.8461, "matched_fragments": 339, "total_fragments": 740, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Piscirickettsiales;f__Piscirickettsiaceae;g__Piscirickettsia", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": 20.062, "optimum_ph": null, "genome_size": 3351088.197, "gc_content": 39.658, "coding_genes": 3174.476, "rRNA16S_genes": 6.0, "tRNA_genes": 56.0, "gram_stain": 0.0, "sporulation": null, "motility": 0.0, "range_salinity": 1.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 1.0, "bacillus_cell_shape": 0.0, "coccus_cell_shape": 1.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Piscirickettsia", "salmonis", "LF-89", "=", "ATCC", "VR-1361" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }