{ "type": "genome", "identifier": "GCF_902500215.1", "organism": "Halomonas lysinitropha", "title": "Halomonas lysinitropha", "description": "na", "data type": "Genome sequencing and assembly", "organization": "INSTITUT PASTEUR", "publication": [ {} ], "properties": { "assembly_accession": "GCF_902500215.1", "bioproject": "PRJNA224116", "biosample": "SAMEA5972740", "wgs_master": "CABVOU000000000.1", "refseq_category": "reference genome", "taxid": "2607506", "species_taxid": "2607506", "organism_name": "Halomonas lysinitropha", "infraspecific_name": "strain=3(2)", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/09/30", "asm_name": "CIP111708", "asm_submitter": "INSTITUT PASTEUR", "gbrs_paired_asm": "GCA_902500215.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/902/500/215/GCF_902500215.1_CIP111708", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3830613", "genome_size_ungapped": "3830424", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "63", "contig_count": "63", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_902500215.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "3604", "protein_coding_gene_count": "3492", "non_coding_gene_count": "86", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-09-30", "dateModified": "2019-09-30", "datePublished": "2019-09-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas lysinitropha" ], "sample_taxid": [ "2607506" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.064 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)": "3830613", "Number of Sequences": "63", "Longest Sequences (bp)": "612597", "N50 (bp)": "216315", "Gap Ratio (%)": "0.005143", "GCcontent (%)": "64.8", "Number of CDSs": "3505", "Average Protein Length": "327.7", "Coding Ratio (%)": "90.0", "Number of rRNAs": "1", "Number of tRNAs": "70", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas lysinitropha", "strain": "strain=3(2)", "accession": "GCA_902500215.1", "taxid": 2607506, "species_taxid": 2607506, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1256, "total_fragments": 1256, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halomonas ventosae", "strain": "strain=CECT 5797", "accession": "GCA_004363555.1", "taxid": 229007, "species_taxid": 229007, "relation_to_type": "type", "validated": true, "ani": 88.7952, "matched_fragments": 945, "total_fragments": 1256, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas daqiaonensis", "strain": "strain=CGMCC 1.9150", "accession": "GCA_900109725.1", "taxid": 650850, "species_taxid": 650850, "relation_to_type": "type", "validated": true, "ani": 88.4471, "matched_fragments": 950, "total_fragments": 1256, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas fontilapidosi", "strain": "strain=CECT 7341", "accession": "GCA_014192285.1", "taxid": 616675, "species_taxid": 616675, "relation_to_type": "type", "validated": true, "ani": 86.7554, "matched_fragments": 927, "total_fragments": 1256, "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, "ani": 85.791, "matched_fragments": 861, "total_fragments": 1256, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas denitrificans", "strain": "strain=DSM 18045", "accession": "GCA_003056305.1", "taxid": 370769, "species_taxid": 370769, "relation_to_type": "type", "validated": true, "ani": 85.3967, "matched_fragments": 867, "total_fragments": 1256, "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": 85.1202, "matched_fragments": 890, "total_fragments": 1256, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas campisalis", "strain": "strain=A4", "accession": "GCA_022341425.1", "taxid": 74661, "species_taxid": 74661, "relation_to_type": "type", "validated": true, "ani": 82.8729, "matched_fragments": 784, "total_fragments": 1256, "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": 81.8722, "matched_fragments": 756, "total_fragments": 1256, "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": 81.1357, "matched_fragments": 666, "total_fragments": 1256, "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": 81.0582, "matched_fragments": 707, "total_fragments": 1256, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_902500215.1", "gtdb_species": "s__Halomonas sp902500215", "ani": 100.0, "matched_fragments": 1256, "total_fragments": 1256, "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_004363555.1", "gtdb_species": "s__Halomonas ventosae", "ani": 88.7744, "matched_fragments": 946, "total_fragments": 1256, "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": "-" }, { "accession": "GCF_900109725.1", "gtdb_species": "s__Halomonas daqiaonensis", "ani": 88.4592, "matched_fragments": 949, "total_fragments": 1256, "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_014192285.1", "gtdb_species": "s__Halomonas fontilapidosi", "ani": 86.7466, "matched_fragments": 928, "total_fragments": 1256, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.17", "min_intra_species_ani": "98.17", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001886615.1", "gtdb_species": "s__Halomonas aestuarii", "ani": 85.7804, "matched_fragments": 861, "total_fragments": 1256, "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_004361885.1", "gtdb_species": "s__Halomonas ventosae_C", "ani": 85.7429, "matched_fragments": 738, "total_fragments": 1256, "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": 85.1528, "matched_fragments": 887, "total_fragments": 1256, "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": 85.119, "matched_fragments": 837, "total_fragments": 1256, "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_900116405.1", "gtdb_species": "s__Halomonas saccharevitans", "ani": 84.9024, "matched_fragments": 810, "total_fragments": 1256, "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", "lysinitropha" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }