{ "type": "genome", "identifier": "GCF_025917315.1", "organism": "Halomonas qaidamensis", "title": "Halomonas qaidamensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Qinghai University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025917315.1", "bioproject": "PRJNA224116", "biosample": "SAMN20568220", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2866211", "species_taxid": "2866211", "organism_name": "Halomonas qaidamensis", "infraspecific_name": "strain=XH36", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/10/31", "asm_name": "ASM2591731v1", "asm_submitter": "Qinghai University", "gbrs_paired_asm": "GCA_025917315.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/917/315/GCF_025917315.1_ASM2591731v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3818310", "genome_size_ungapped": "3818310", "gc_percent": "52.000000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025917315.1-RS_2024_11_26", "annotation_date": "2024-11-26", "total_gene_count": "3472", "protein_coding_gene_count": "3374", "non_coding_gene_count": "83", "pubmed_id": "35243586" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-10-31", "dateModified": "2022-10-31", "datePublished": "2022-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas qaidamensis" ], "sample_taxid": [ "2866211" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Qinghai" ], "sample_host_location_id": [], "data_size": "1.082 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)": "3818310", "Number of Sequences": "2", "Longest Sequences (bp)": "3772457", "N50 (bp)": "3772457", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.0", "Number of CDSs": "3399", "Average Protein Length": "332.0", "Coding Ratio (%)": "88.7", "Number of rRNAs": "18", "Number of tRNAs": "61", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas alkaliphila", "strain": "strain=DSM 16354", "accession": "GCA_016107625.1", "taxid": 272774, "species_taxid": 272774, "relation_to_type": "type", "validated": true, "ani": 87.1079, "matched_fragments": 1018, "total_fragments": 1272, "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": 87.0723, "matched_fragments": 1010, "total_fragments": 1272, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas hydrothermalis", "strain": "strain=Slthf2", "accession": "GCA_011399095.1", "taxid": 115561, "species_taxid": 115561, "relation_to_type": "type", "validated": true, "ani": 85.8438, "matched_fragments": 944, "total_fragments": 1272, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas venusta", "strain": "strain=DSM 4743", "accession": "GCA_016107635.1", "taxid": 44935, "species_taxid": 44935, "relation_to_type": "type", "validated": true, "ani": 85.7921, "matched_fragments": 960, "total_fragments": 1272, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas venusta", "strain": "strain=NBRC 102221", "accession": "GCA_007989605.1", "taxid": 44935, "species_taxid": 44935, "relation_to_type": "type", "validated": true, "ani": 85.7224, "matched_fragments": 945, "total_fragments": 1272, "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": 84.2136, "matched_fragments": 902, "total_fragments": 1272, "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": 84.0035, "matched_fragments": 835, "total_fragments": 1272, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas johnsoniae", "strain": "strain=KCTC 22157", "accession": "GCA_014651795.1", "taxid": 502832, "species_taxid": 502832, "relation_to_type": "type", "validated": true, "ani": 79.5429, "matched_fragments": 464, "total_fragments": 1272, "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": 79.4179, "matched_fragments": 398, "total_fragments": 1272, "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": 79.309, "matched_fragments": 377, "total_fragments": 1272, "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": 79.1381, "matched_fragments": 359, "total_fragments": 1272, "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": 79.0247, "matched_fragments": 393, "total_fragments": 1272, "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": 77.4845, "matched_fragments": 132, "total_fragments": 1272, "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": 77.4636, "matched_fragments": 133, "total_fragments": 1272, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000712975.1", "gtdb_species": "s__Halomonas alkaliantarctica_A", "ani": 99.081, "matched_fragments": 1155, "total_fragments": 1272, "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_002082565.1", "gtdb_species": "s__Halomonas sp002082565", "ani": 87.6804, "matched_fragments": 1051, "total_fragments": 1272, "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": 87.1662, "matched_fragments": 1038, "total_fragments": 1272, "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_016107625.1", "gtdb_species": "s__Halomonas alkaliphila", "ani": 87.1181, "matched_fragments": 1017, "total_fragments": 1272, "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": "GCA_007116835.1", "gtdb_species": "s__Halomonas sp007116835", "ani": 86.5048, "matched_fragments": 439, "total_fragments": 1272, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.44", "min_intra_species_ani": "98.44", "mean_intra_species_af": "0.71", "min_intra_species_af": "0.71", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_007989605.1", "gtdb_species": "s__Halomonas venusta", "ani": 85.7224, "matched_fragments": 945, "total_fragments": 1272, "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": "-" }, { "accession": "GCF_003989795.1", "gtdb_species": "s__Halomonas andesensis", "ani": 84.2486, "matched_fragments": 900, "total_fragments": 1272, "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_013415115.1", "gtdb_species": "s__Halomonas zhaodongensis", "ani": 83.9964, "matched_fragments": 836, "total_fragments": 1272, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.15", "min_intra_species_ani": "99.15", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003002925.1", "gtdb_species": "s__Halomonas songnenensis", "ani": 79.1259, "matched_fragments": 361, "total_fragments": 1272, "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", "qaidamensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }