{ "type": "genome", "identifier": "GCF_000238295.3", "organism": "Pseudoalteromonas rubra", "title": "Pseudoalteromonas rubra", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Shandong University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000238295.3", "bioproject": "PRJNA224116", "biosample": "SAMN03380246", "wgs_master": "AHCD00000000.3", "refseq_category": "reference genome", "taxid": "43658", "species_taxid": "43658", "organism_name": "Pseudoalteromonas rubra", "infraspecific_name": "strain=DSM 6842", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/10/02", "asm_name": "ASM23829v4", "asm_submitter": "Shandong University", "gbrs_paired_asm": "GCA_000238295.4", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/238/295/GCF_000238295.3_ASM23829v4", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6143755", "genome_size_ungapped": "6143755", "gc_percent": "48.000000", "replicon_count": "1", "scaffold_count": "44", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000238295.3-RS_2024_04_06", "annotation_date": "2024-04-06", "total_gene_count": "5274", "protein_coding_gene_count": "4956", "non_coding_gene_count": "243", "pubmed_id": "22374963" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-10-02", "dateModified": "2020-10-02", "datePublished": "2020-10-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudoalteromonas rubra" ], "sample_taxid": [ "43658" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "France: Nice" ], "sample_host_location_id": [], "data_size": "1.723 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)": "6143755", "Number of Sequences": "44", "Longest Sequences (bp)": "1388597", "N50 (bp)": "574146", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "47.8", "Number of CDSs": "5036", "Average Protein Length": "351.0", "Coding Ratio (%)": "86.3", "Number of rRNAs": "7", "Number of tRNAs": "239", "Number of CRISPRs": "8" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudoalteromonas rubra", "strain": "strain=DSM 6842", "accession": "GCA_000238295.4", "taxid": 43658, "species_taxid": 43658, "relation_to_type": "suspected-type", "validated": true, "ani": 100.0, "matched_fragments": 2027, "total_fragments": 2031, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudoalteromonas galatheae", "strain": "strain=S4498", "accession": "GCA_005886105.2", "taxid": 579562, "species_taxid": 579562, "relation_to_type": "type", "validated": true, "ani": 79.5738, "matched_fragments": 301, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas byunsanensis", "strain": "strain=JCM 12483", "accession": "GCA_001854475.1", "taxid": 327939, "species_taxid": 327939, "relation_to_type": "type", "validated": true, "ani": 79.3589, "matched_fragments": 229, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas luteoviolacea", "strain": "strain=CH130", "accession": "GCA_014925325.1", "taxid": 43657, "species_taxid": 43657, "relation_to_type": "suspected-type", "validated": true, "ani": 79.1011, "matched_fragments": 347, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas phenolica", "strain": "strain=O-BC30", "accession": "GCA_014925335.1", "taxid": 161398, "species_taxid": 161398, "relation_to_type": "suspected-type", "validated": true, "ani": 79.0837, "matched_fragments": 257, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas phenolica", "strain": "strain=KCTC 12086", "accession": "GCA_001444405.1", "taxid": 161398, "species_taxid": 161398, "relation_to_type": "suspected-type", "validated": true, "ani": 78.9846, "matched_fragments": 258, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas luteoviolacea", "strain": "strain=DSM 6061", "accession": "GCA_001625655.1", "taxid": 43657, "species_taxid": 43657, "relation_to_type": "suspected-type", "validated": true, "ani": 78.892, "matched_fragments": 338, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas phenolica", "strain": "strain=O-BC30", "accession": "GCA_004103265.1", "taxid": 161398, "species_taxid": 161398, "relation_to_type": "suspected-type", "validated": true, "ani": 78.8203, "matched_fragments": 232, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas profundi", "strain": "strain=CGMCC 1.15394", "accession": "GCA_014642695.1", "taxid": 1774956, "species_taxid": 1774956, "relation_to_type": "type", "validated": true, "ani": 78.4182, "matched_fragments": 185, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudoalteromonas rhizosphaerae", "strain": "strain=RA15", "accession": "GCA_902498845.1", "taxid": 2518973, "species_taxid": 2518973, "relation_to_type": "type", "validated": true, "ani": 77.8442, "matched_fragments": 175, "total_fragments": 2031, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { 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"mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005886805.2", "gtdb_species": "s__Pseudoalteromonas rubra_D", "ani": 92.9326, "matched_fragments": 1731, "total_fragments": 2031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.21", "min_intra_species_ani": "98.19", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000967655.1", "gtdb_species": "s__Pseudoalteromonas rubra_A", "ani": 84.4929, "matched_fragments": 1389, "total_fragments": 2031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas", "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_017742995.1", "gtdb_species": "s__Pseudoalteromonas viridis", "ani": 84.4319, "matched_fragments": 1378, "total_fragments": 2031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.83", "min_intra_species_ani": "95.16", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.87", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_005887095.1", "gtdb_species": "s__Pseudoalteromonas rubra_E", "ani": 84.0896, "matched_fragments": 1310, "total_fragments": 2031, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", 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0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pseudoalteromonas", "rubra" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }