{ "type": "genome", "identifier": "GCF_013183775.1", "organism": "Halomonas hibernica", "title": "Halomonas hibernica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University College Cork", "publication": [ {} ], "properties": { "assembly_accession": "GCF_013183775.1", "bioproject": "PRJNA224116", "biosample": "SAMN12125540", "wgs_master": "VIFN00000000.1", "refseq_category": "reference genome", "taxid": "2591147", "species_taxid": "2591147", "organism_name": "Halomonas hibernica", "infraspecific_name": "strain=B1.N12", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/05/28", "asm_name": "ASM1318377v1", "asm_submitter": "University College Cork", "gbrs_paired_asm": "GCA_013183775.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/183/775/GCF_013183775.1_ASM1318377v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3769243", "genome_size_ungapped": "3769243", "gc_percent": "54.000000", "replicon_count": "0", "scaffold_count": "43", "contig_count": "43", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_013183775.1-RS_2024_11_26", "annotation_date": "2024-11-26", "total_gene_count": "3569", "protein_coding_gene_count": "3458", "non_coding_gene_count": "63", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-05-28", "dateModified": "2020-05-28", "datePublished": "2020-05-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas hibernica" ], "sample_taxid": [ "2591147" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Ireland" ], "sample_host_location_id": [], "data_size": "1.074 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)": "3769243", "Number of Sequences": "43", "Longest Sequences (bp)": "907559", "N50 (bp)": "308266", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.0", "Number of CDSs": "3519", "Average Protein Length": "313.4", "Coding Ratio (%)": "87.8", "Number of rRNAs": "2", "Number of tRNAs": "57", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas zhanjiangensis", "strain": "strain=DSM 21076", "accession": "GCA_000377665.1", "taxid": 1121960, "species_taxid": 1121960, "relation_to_type": "type", "validated": true, "ani": 84.0184, "matched_fragments": 854, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas nanhaiensis", "strain": "strain=JCM 18142", "accession": "GCA_003990185.1", "taxid": 1258546, "species_taxid": 1258546, "relation_to_type": "type", "validated": true, "ani": 82.3752, "matched_fragments": 726, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas populi", "strain": "strain=MC", "accession": "GCA_003989825.1", "taxid": 2498858, "species_taxid": 2498858, "relation_to_type": "type", "validated": true, "ani": 82.3158, "matched_fragments": 745, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas songnenensis", "strain": "strain=CGMCC 1.12152", "accession": "GCA_003002925.1", "taxid": 1176243, "species_taxid": 1176243, "relation_to_type": "type", "validated": true, "ani": 81.145, "matched_fragments": 636, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lutescens", "strain": "strain=CGMCC 1.15122", "accession": "GCA_014640815.1", "taxid": 1602943, "species_taxid": 1602943, "relation_to_type": "type", "validated": true, "ani": 79.8811, "matched_fragments": 437, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas meridiana", "strain": "strain=NBRC 15608", "accession": "GCA_006540125.1", "taxid": 29570, "species_taxid": 29570, "relation_to_type": "type", "validated": true, "ani": 79.869, "matched_fragments": 416, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aquamarina", "strain": "strain=558", "accession": "GCA_900110265.1", "taxid": 77097, "species_taxid": 77097, "relation_to_type": "type", "validated": true, "ani": 79.8181, "matched_fragments": 440, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lionensis", "strain": "strain=RHS90", "accession": "GCA_002087295.1", "taxid": 1144478, "species_taxid": 1144478, "relation_to_type": "type", "validated": true, "ani": 79.6699, "matched_fragments": 430, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas zhaodongensis", "strain": "strain=NEAU-ST10-25", "accession": "GCA_013415115.1", "taxid": 1176240, "species_taxid": 1176240, "relation_to_type": "type", "validated": true, "ani": 79.3918, "matched_fragments": 385, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas andesensis", "strain": "strain=DSM 19434", "accession": "GCA_003989795.1", "taxid": 447567, "species_taxid": 447567, "relation_to_type": "type", "validated": true, "ani": 79.1883, "matched_fragments": 363, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas profundi", "strain": "strain=MT13", "accession": "GCA_019504685.1", "taxid": 2852117, "species_taxid": 2852117, "relation_to_type": "type", "validated": true, "ani": 79.0153, "matched_fragments": 450, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas boliviensis", "strain": "strain=LC1", "accession": "GCA_000236035.1", "taxid": 223527, "species_taxid": 223527, "relation_to_type": "type", "validated": true, "ani": 78.9702, "matched_fragments": 467, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas profundi", "strain": "strain=MT13", "accession": "GCA_019722725.1", "taxid": 2852117, "species_taxid": 2852117, "relation_to_type": "type", "validated": true, "ani": 78.9467, "matched_fragments": 453, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas boliviensis", "strain": "strain=LC1", "accession": "GCA_002265845.1", "taxid": 223527, "species_taxid": 223527, "relation_to_type": "type", "validated": true, "ani": 78.9429, "matched_fragments": 475, "total_fragments": 1233, "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": 77.6674, "matched_fragments": 169, "total_fragments": 1233, "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": 77.6264, "matched_fragments": 187, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900163645.1", "gtdb_species": "s__Halomonas sp900163645", "ani": 95.53, "matched_fragments": 990, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.99", "min_intra_species_ani": "95.49", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.80", "num_clustered_genomes": 6, "status": "conclusive" }, { "accession": "GCF_014897985.1", "gtdb_species": "s__Halomonas sp014897985", "ani": 84.1986, "matched_fragments": 830, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.34", "min_intra_species_ani": "98.34", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000377665.1", "gtdb_species": "s__Halomonas zhanjiangensis", "ani": 84.0407, "matched_fragments": 852, "total_fragments": 1233, "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": "GCA_017983445.1", "gtdb_species": "s__Halomonas sp017983445", "ani": 83.2353, "matched_fragments": 799, "total_fragments": 1233, "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_003990185.1", "gtdb_species": "s__Halomonas nanhaiensis", "ani": 82.3752, "matched_fragments": 726, "total_fragments": 1233, "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_003990195.1", "gtdb_species": "s__Halomonas sp003990195", "ani": 82.2769, "matched_fragments": 754, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "98.34", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003002925.1", "gtdb_species": "s__Halomonas songnenensis", "ani": 81.152, "matched_fragments": 635, "total_fragments": 1233, "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_014640815.1", "gtdb_species": "s__Halomonas lutescens", "ani": 79.8811, "matched_fragments": 437, "total_fragments": 1233, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.121, "cell_length": 0.276, "doubling_h": 0.239, "growth_tmp": 30.353, "optimum_tmp": 31.375, "optimum_ph": 7.642, "genome_size": 3925920.429, "gc_content": 60.3, "coding_genes": 3582.761, "rRNA16S_genes": 3.8, "tRNA_genes": 63.428, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.808, "range_salinity": 1.0, "facultative_respiration": 0.164, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.835, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.961, "coccus_cell_shape": 0.019, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.019, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Halomonas", "hibernica" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }