{ "type": "genome", "identifier": "GCF_011399095.1", "organism": "Halomonas hydrothermalis", "title": "Halomonas hydrothermalis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Keio University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011399095.1", "bioproject": "PRJNA224116", "biosample": "SAMN14086256", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "115561", "species_taxid": "115561", "organism_name": "Halomonas hydrothermalis", "infraspecific_name": "strain=Slthf2", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/10", "asm_name": "ASM1139909v1", "asm_submitter": "Keio University", "gbrs_paired_asm": "GCA_011399095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/399/095/GCF_011399095.1_ASM1139909v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4120823", "genome_size_ungapped": "4120823", "gc_percent": "53.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011399095.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "3802", "protein_coding_gene_count": "3646", "non_coding_gene_count": "82", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-10", "dateModified": "2020-03-10", "datePublished": "2020-03-10", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas hydrothermalis" ], "sample_taxid": [ "115561" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Pacific Ocean" ], "sample_host_location_id": [], "data_size": "1.166 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)": "4120823", "Number of Sequences": "1", "Longest Sequences (bp)": "4120823", "N50 (bp)": "4120823", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "53.2", "Number of CDSs": "3761", "Average Protein Length": "323.4", "Coding Ratio (%)": "88.5", "Number of rRNAs": "18", "Number of tRNAs": "60", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas hydrothermalis", "strain": "strain=Slthf2", "accession": "GCA_011399095.1", "taxid": 115561, "species_taxid": 115561, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1369, "total_fragments": 1373, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Halomonas venusta", "strain": "strain=DSM 4743", "accession": "GCA_016107635.1", "taxid": 44935, "species_taxid": 44935, "relation_to_type": "type", "validated": true, "ani": 96.6238, "matched_fragments": 1153, "total_fragments": 1373, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Halomonas venusta", "strain": "strain=NBRC 102221", "accession": "GCA_007989605.1", "taxid": 44935, "species_taxid": 44935, "relation_to_type": "type", "validated": true, "ani": 96.6059, "matched_fragments": 1141, "total_fragments": 1373, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Halomonas alkaliphila", "strain": "strain=DSM 16354", "accession": "GCA_016107625.1", "taxid": 272774, "species_taxid": 272774, "relation_to_type": "type", "validated": true, "ani": 92.8784, "matched_fragments": 1096, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas humidisoli", "strain": "strain=WN018", "accession": "GCA_002286955.1", "taxid": 2032624, "species_taxid": 2032624, "relation_to_type": "type", "validated": true, "ani": 92.7884, "matched_fragments": 1076, "total_fragments": 1373, "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": 79.0827, "matched_fragments": 415, "total_fragments": 1373, "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": 78.8511, "matched_fragments": 128, "total_fragments": 1373, "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": 77.834, "matched_fragments": 138, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas kenyensis", "strain": "strain=DSM 17331", "accession": "GCA_022341445.1", "taxid": 321266, "species_taxid": 321266, "relation_to_type": "type", "validated": true, "ani": 77.5077, "matched_fragments": 127, "total_fragments": 1373, "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": 76.9831, "matched_fragments": 154, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_007989605.1", "gtdb_species": "s__Halomonas venusta", "ani": 96.6059, "matched_fragments": 1141, "total_fragments": 1373, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.80", "min_intra_species_ani": "96.64", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.83", "num_clustered_genomes": 8, "status": "conclusive" }, { "accession": "GCF_016107625.1", "gtdb_species": "s__Halomonas alkaliphila", "ani": 92.8784, "matched_fragments": 1096, "total_fragments": 1373, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.32", "min_intra_species_ani": "95.46", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.80", "num_clustered_genomes": 12, "status": "-" }, { "accession": "GCF_002082565.1", "gtdb_species": "s__Halomonas sp002082565", "ani": 90.117, "matched_fragments": 1077, "total_fragments": 1373, "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_000219565.1", "gtdb_species": "s__Halomonas sp000219565", "ani": 88.5393, "matched_fragments": 1042, "total_fragments": 1373, "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_000712975.1", "gtdb_species": "s__Halomonas alkaliantarctica_A", "ani": 85.8229, "matched_fragments": 916, "total_fragments": 1373, "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_003989795.1", "gtdb_species": "s__Halomonas andesensis", "ani": 84.9039, "matched_fragments": 881, "total_fragments": 1373, "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": 0.176, "cell_length": 0.397, "doubling_h": 0.239, "growth_tmp": 29.0, "optimum_tmp": 30.0, "optimum_ph": 7.5, "genome_size": 3887140.5, "gc_content": 60.2, "coding_genes": 3520.0, "rRNA16S_genes": 3.8, "tRNA_genes": 61.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 1.0, "facultative_respiration": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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", "hydrothermalis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }