{ "type": "genome", "identifier": "GCF_003987065.1", "organism": "Pseudidiomarina insulisalsae", "title": "Pseudidiomarina insulisalsae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The Third Institute of Oceanography, Key Laboratory of Marine Biogenetic Resources", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003987065.1", "bioproject": "PRJNA224116", "biosample": "SAMN08102259", "wgs_master": "PIPY00000000.1", "refseq_category": "reference genome", "taxid": "575789", "species_taxid": "575789", "organism_name": "Pseudidiomarina insulisalsae", "infraspecific_name": "strain=CVS-6", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/12/31", "asm_name": "ASM398706v1", "asm_submitter": "The Third Institute of Oceanography, Key Laboratory of Marine Biogenetic Resources", "gbrs_paired_asm": "GCA_003987065.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/987/065/GCF_003987065.1_ASM398706v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2560959", "genome_size_ungapped": "2560959", "gc_percent": "52.500000", "replicon_count": "0", "scaffold_count": "19", "contig_count": "19", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003987065.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "2409", "protein_coding_gene_count": "2336", "non_coding_gene_count": "63", "pubmed_id": "30364313" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-12-31", "dateModified": "2018-12-31", "datePublished": "2018-12-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Pseudidiomarina insulisalsae" ], "sample_taxid": [ "575789" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Cape Verde: Island of Sal" ], "sample_host_location_id": [], "data_size": "0.732 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)": "2560959", "Number of Sequences": "19", "Longest Sequences (bp)": "350757", "N50 (bp)": "207837", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.3", "Number of CDSs": "2343", "Average Protein Length": "341.3", "Coding Ratio (%)": "93.7", "Number of rRNAs": "6", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pseudidiomarina insulisalsae", "strain": "strain=CVS-6", "accession": "GCA_003987065.1", "taxid": 575789, "species_taxid": 575789, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 842, "total_fragments": 843, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudidiomarina aquimaris", "strain": "strain=SW15", "accession": "GCA_003987395.1", "taxid": 641841, "species_taxid": 641841, "relation_to_type": "type", "validated": true, "ani": 79.9457, "matched_fragments": 387, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina homiensis", "strain": "strain=PO-M2", "accession": "GCA_003987225.1", "taxid": 364198, "species_taxid": 364198, "relation_to_type": "type", "validated": true, "ani": 79.8309, "matched_fragments": 370, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina halophila", "strain": "strain=BH195", "accession": "GCA_003987215.1", "taxid": 1449799, "species_taxid": 1449799, "relation_to_type": "type", "validated": true, "ani": 79.256, "matched_fragments": 333, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina sediminum", "strain": "strain=c121", "accession": "GCA_003987265.1", "taxid": 431675, "species_taxid": 431675, "relation_to_type": "type", "validated": true, "ani": 79.1265, "matched_fragments": 300, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina marina", "strain": "strain=PIM1", "accession": "GCA_003987045.1", "taxid": 502366, "species_taxid": 502366, "relation_to_type": "type", "validated": true, "ani": 79.122, "matched_fragments": 163, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina sediminum", "strain": "strain=DSM 21906", "accession": "GCA_000423165.1", "taxid": 431675, "species_taxid": 431675, "relation_to_type": "type", "validated": true, "ani": 79.0685, "matched_fragments": 298, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina atlantica", "strain": "strain=MCCC 1A10513", "accession": "GCA_000753735.1", "taxid": 1517416, "species_taxid": 1517416, "relation_to_type": "type", "validated": true, "ani": 78.7887, "matched_fragments": 281, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina salinarum", "strain": "strain=ISL-52", "accession": "GCA_003987105.1", "taxid": 435908, "species_taxid": 435908, "relation_to_type": "type", "validated": true, "ani": 78.7284, "matched_fragments": 196, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudidiomarina salinarum", "strain": "strain=ISL-52", "accession": "GCA_000753715.1", "taxid": 435908, "species_taxid": 435908, "relation_to_type": "type", "validated": true, "ani": 78.5565, "matched_fragments": 196, "total_fragments": 843, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003987065.1", "gtdb_species": "s__Pseudidiomarina insulisalsae", "ani": 100.0, "matched_fragments": 842, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_003987395.1", "gtdb_species": "s__Pseudidiomarina aquimaris", "ani": 79.96, "matched_fragments": 386, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.26", "min_intra_species_ani": "97.14", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.77", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003987225.1", "gtdb_species": "s__Pseudidiomarina homiensis", "ani": 79.8309, "matched_fragments": 370, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_003987215.1", "gtdb_species": "s__Pseudidiomarina halophila", "ani": 79.2419, "matched_fragments": 334, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_003987045.1", "gtdb_species": "s__Pseudidiomarina marina", "ani": 79.0822, "matched_fragments": 165, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.46", "min_intra_species_ani": "97.46", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000423165.1", "gtdb_species": "s__Pseudidiomarina sediminum", "ani": 79.0589, "matched_fragments": 297, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_000753735.1", "gtdb_species": "s__Pseudidiomarina atlantica", "ani": 78.7887, "matched_fragments": 281, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_900116895.1", "gtdb_species": "s__Pseudidiomarina donghaiensis", "ani": 78.7675, "matched_fragments": 183, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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": "GCF_009734345.1", "gtdb_species": "s__Pseudidiomarina andamanensis", "ani": 78.7244, "matched_fragments": 185, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_000753715.1", "gtdb_species": "s__Pseudidiomarina salinarum", "ani": 78.5565, "matched_fragments": 196, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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": "GCA_018222985.1", "gtdb_species": "s__Pseudidiomarina sp018222985", "ani": 78.4419, "matched_fragments": 178, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina", "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_003987185.1", "gtdb_species": "s__Idiomarina aquatica", "ani": 77.8338, "matched_fragments": 107, "total_fragments": 843, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.08", "min_intra_species_ani": "99.08", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Pseudidiomarina", "insulisalsae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }