{ "type": "genome", "identifier": "GCF_900109905.1", "organism": "Halomonas caseinilytica", "title": "Halomonas caseinilytica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900109905.1", "bioproject": "PRJNA224116", "biosample": "SAMN04487952", "wgs_master": "FOBT00000000.1", "refseq_category": "na", "taxid": "438744", "species_taxid": "438744", "organism_name": "Halomonas caseinilytica", "infraspecific_name": "strain=CGMCC 1.6773", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2617270935 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900109905.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/109/905/GCF_900109905.1_IMG-taxon_2617270935_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": "3569348", "genome_size_ungapped": "3568798", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "28", "contig_count": "28", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900109905.1-RS_2024_07_25", "annotation_date": "2024-07-25", "total_gene_count": "3430", "protein_coding_gene_count": "3345", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas caseinilytica" ], "sample_taxid": [ "438744" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "0.995 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)": "3569348", "Number of Sequences": "28", "Longest Sequences (bp)": "521303", "N50 (bp)": "240611", "Gap Ratio (%)": "0.015409", "GCcontent (%)": "63.4", "Number of CDSs": "3340", "Average Protein Length": "317.4", "Coding Ratio (%)": "89.1", "Number of rRNAs": "4", "Number of tRNAs": "54", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas caseinilytica", "strain": "strain=CGMCC 1.6773", "accession": "GCA_900109905.1", "taxid": 438744, "species_taxid": 438744, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1172, "total_fragments": 1175, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halomonas caseinilytica", "strain": "strain=JCM 14802", "accession": "GCA_001662305.1", "taxid": 438744, "species_taxid": 438744, "relation_to_type": "type", "validated": true, "ani": 99.9897, "matched_fragments": 1161, "total_fragments": 1175, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halomonas elongata", "strain": "strain=type strain: DSM 2581", "accession": "GCA_000196875.2", "taxid": 2746, "species_taxid": 2746, "relation_to_type": "type", "validated": true, "ani": 88.7759, "matched_fragments": 1023, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas stenophila", "strain": "strain=CECT 7744", "accession": "GCA_014192275.1", "taxid": 795312, "species_taxid": 795312, "relation_to_type": "type", "validated": true, "ani": 82.7722, "matched_fragments": 775, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas nitroreducens", "strain": "strain=11S", "accession": "GCA_003966155.1", "taxid": 447425, "species_taxid": 447425, "relation_to_type": "type", "validated": true, "ani": 82.6994, "matched_fragments": 735, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas halophila", "strain": "strain=NBRC 102604", "accession": "GCA_007989465.1", "taxid": 29573, "species_taxid": 29573, "relation_to_type": "type", "validated": true, "ani": 82.6552, "matched_fragments": 738, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas smyrnensis", "strain": "strain=AAD6", "accession": "GCA_000265245.2", "taxid": 720605, "species_taxid": 720605, "relation_to_type": "type", "validated": true, "ani": 82.5972, "matched_fragments": 712, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lysinitropha", "strain": "strain=3(2)", "accession": "GCA_902500215.1", "taxid": 2607506, "species_taxid": 2607506, "relation_to_type": "type", "validated": true, "ani": 80.9033, "matched_fragments": 599, "total_fragments": 1175, "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": 80.8826, "matched_fragments": 599, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas gudaonensis", "strain": "strain=CGMCC 1.6133", "accession": "GCA_900100195.1", "taxid": 376427, "species_taxid": 376427, "relation_to_type": "type", "validated": true, "ani": 80.5336, "matched_fragments": 585, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas alkalisoli", "strain": "strain=M5N1S17", "accession": "GCA_021412585.1", "taxid": 2907158, "species_taxid": 2907158, "relation_to_type": "type", "validated": true, "ani": 80.3701, "matched_fragments": 567, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aerodenitrificans", "strain": "strain=MCCC 1A11058", "accession": "GCA_021404405.1", "taxid": 2733483, "species_taxid": 2733483, "relation_to_type": "type", "validated": true, "ani": 80.3441, "matched_fragments": 589, "total_fragments": 1175, "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": 80.2527, "matched_fragments": 583, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromohalobacter japonicus", "strain": "strain=CECT 7219", "accession": "GCA_023061175.1", "taxid": 223900, "species_taxid": 223900, "relation_to_type": "type", "validated": true, "ani": 79.0933, "matched_fragments": 393, "total_fragments": 1175, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001662305.1", "gtdb_species": "s__Halomonas caseinilytica", "ani": 99.9897, "matched_fragments": 1161, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.18", "min_intra_species_ani": "98.28", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_000196875.2", "gtdb_species": "s__Halomonas elongata", "ani": 88.7759, "matched_fragments": 1023, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "98.56", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_008274785.1", "gtdb_species": "s__Halomonas eurihalina", "ani": 88.5574, "matched_fragments": 1000, "total_fragments": 1175, "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_014192275.1", "gtdb_species": "s__Halomonas stenophila", "ani": 82.8119, "matched_fragments": 771, "total_fragments": 1175, "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_006540005.1", "gtdb_species": "s__Halomonas halmophila", "ani": 82.7415, "matched_fragments": 719, "total_fragments": 1175, "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_003966155.1", "gtdb_species": "s__Halomonas nitroreducens", "ani": 82.7023, "matched_fragments": 734, "total_fragments": 1175, "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_002549795.1", "gtdb_species": "s__Halomonas beimenensis", "ani": 82.6762, "matched_fragments": 700, "total_fragments": 1175, "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_007989465.1", "gtdb_species": "s__Halomonas halophila", "ani": 82.6708, "matched_fragments": 736, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.43", "min_intra_species_ani": "97.59", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.89", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_000265245.1", "gtdb_species": "s__Halomonas smyrnensis", "ani": 82.6066, "matched_fragments": 710, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.45", "min_intra_species_ani": "98.45", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900100195.1", "gtdb_species": "s__Halomonas gudaonensis", "ani": 80.5709, "matched_fragments": 581, "total_fragments": 1175, "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_015595025.1", "gtdb_species": "s__Halomonas sp015595025", "ani": 80.4237, "matched_fragments": 565, "total_fragments": 1175, "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_000620045.1", "gtdb_species": "s__Halomonas halodenitrificans", "ani": 80.3094, "matched_fragments": 518, "total_fragments": 1175, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": 0.146, "doubling_h": 0.239, "growth_tmp": 28.0, "optimum_tmp": 30.0, "optimum_ph": 7.5, "genome_size": 3534344.333, "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": 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": [ "Halomonas", "caseinilytica" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }