{ "type": "genome", "identifier": "GCF_900116405.1", "organism": "Halomonas saccharevitans", "title": "Halomonas saccharevitans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900116405.1", "bioproject": "PRJNA224116", "biosample": "SAMN04487956", "wgs_master": "FPAQ00000000.1", "refseq_category": "na", "taxid": "416872", "species_taxid": "416872", "organism_name": "Halomonas saccharevitans", "infraspecific_name": "strain=CGMCC 1.6493", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2617270933 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900116405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/116/405/GCF_900116405.1_IMG-taxon_2617270933_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3681289", "genome_size_ungapped": "3678813", "gc_percent": "67.000000", "replicon_count": "0", "scaffold_count": "90", "contig_count": "90", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900116405.1-RS_2024_05_03", "annotation_date": "2024-05-03", "total_gene_count": "3543", "protein_coding_gene_count": "3428", "non_coding_gene_count": "70", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas saccharevitans" ], "sample_taxid": [ "416872" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.012 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)": "3681289", "Number of Sequences": "90", "Longest Sequences (bp)": "253238", "N50 (bp)": "84047", "Gap Ratio (%)": "0.067259", "GCcontent (%)": "67.1", "Number of CDSs": "3412", "Average Protein Length": "317.5", "Coding Ratio (%)": "88.3", "Number of rRNAs": "4", "Number of tRNAs": "56", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas saccharevitans", "strain": "strain=CGMCC 1.6493", "accession": "GCA_900116405.1", "taxid": 416872, "species_taxid": 416872, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1179, "total_fragments": 1182, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halomonas denitrificans", "strain": "strain=DSM 18045", "accession": "GCA_003056305.1", "taxid": 370769, "species_taxid": 370769, "relation_to_type": "type", "validated": true, "ani": 92.1526, "matched_fragments": 992, "total_fragments": 1182, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas urmiana", "strain": "strain=TBZ3", "accession": "GCA_005780185.1", "taxid": 490901, "species_taxid": 490901, "relation_to_type": "type", "validated": true, "ani": 92.1028, "matched_fragments": 954, "total_fragments": 1182, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aestuarii", "strain": "strain=Hb3", "accession": "GCA_001886615.1", "taxid": 1897729, "species_taxid": 1897729, "relation_to_type": "type", "validated": true, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas sulfidoxydans", "strain": "strain=MCCC 1A11059", "accession": "GCA_017868775.1", "taxid": 2733484, "species_taxid": 2733484, "relation_to_type": "type", "validated": true, "ani": 83.0278, "matched_fragments": 728, "total_fragments": 1182, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas ethanolica", "strain": "strain=MCCC 1A11081", "accession": "GCA_021404305.1", "taxid": 2733486, "species_taxid": 2733486, "relation_to_type": "type", "validated": true, "ani": 82.1793, "matched_fragments": 706, "total_fragments": 1182, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas tianxiuensis", "strain": "strain=BC-M4-5", "accession": "GCA_009834345.1", "taxid": 2497861, "species_taxid": 2497861, "relation_to_type": "type", "validated": true, "ani": 81.723, "matched_fragments": 683, "total_fragments": 1182, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900116405.1", "gtdb_species": "s__Halomonas saccharevitans", "ani": 100.0, "matched_fragments": 1179, "total_fragments": 1182, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_003056305.1", "gtdb_species": "s__Halomonas denitrificans", "ani": 92.1526, "matched_fragments": 992, "total_fragments": 1182, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_005780185.1", "gtdb_species": "s__Halomonas urmiana", "ani": 92.1028, "matched_fragments": 954, "total_fragments": 1182, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_009363755.1", "gtdb_species": "s__Halomonas sp009363755", "ani": 91.0387, "matched_fragments": 936, "total_fragments": 1182, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_001886615.1", "gtdb_species": "s__Halomonas aestuarii", "ani": 89.0281, "matched_fragments": 877, "total_fragments": 1182, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_004363555.1", "gtdb_species": "s__Halomonas ventosae", "ani": 87.3225, "matched_fragments": 893, "total_fragments": 1182, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.59", "min_intra_species_ani": "95.59", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.0, "cell_length": 0.477, "doubling_h": 0.239, "growth_tmp": 29.0, "optimum_tmp": 30.0, "optimum_ph": 7.5, "genome_size": 3681289.0, "gc_content": 60.3, "coding_genes": 3582.761, "rRNA16S_genes": 3.8, "tRNA_genes": 63.428, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 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": 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": [ "Halomonas", "saccharevitans" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }