{ "type": "genome", "identifier": "GCF_024790395.1", "organism": "Halomonas dongshanensis", "title": "Halomonas dongshanensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Fujian Institute of Subtropical Botany", "publication": [ {} ], "properties": { "assembly_accession": "GCF_024790395.1", "bioproject": "PRJNA224116", "biosample": "SAMN22814163", "wgs_master": "JAJISC000000000.1", "refseq_category": "reference genome", "taxid": "2890835", "species_taxid": "2890835", "organism_name": "Halomonas dongshanensis", "infraspecific_name": "strain=yzlin-01", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/08/30", "asm_name": "ASM2479039v1", "asm_submitter": "Fujian Institute of Subtropical Botany", "gbrs_paired_asm": "GCA_024790395.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/024/790/395/GCF_024790395.1_ASM2479039v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3934791", "genome_size_ungapped": "3934697", "gc_percent": "60.000000", "replicon_count": "0", "scaffold_count": "15", "contig_count": "15", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_024790395.1-RS_2024_05_13", "annotation_date": "2024-05-13", "total_gene_count": "3654", "protein_coding_gene_count": "3563", "non_coding_gene_count": "68", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-08-30", "dateModified": "2022-08-30", "datePublished": "2022-08-30", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas dongshanensis" ], "sample_taxid": [ "2890835" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Dongshan Bay in Fujian" ], "sample_host_location_id": [], "data_size": "1.109 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)": "3934791", "Number of Sequences": "15", "Longest Sequences (bp)": "771685", "N50 (bp)": "499649", "Gap Ratio (%)": "0.002389", "GCcontent (%)": "60.0", "Number of CDSs": "3584", "Average Protein Length": "327.8", "Coding Ratio (%)": "89.6", "Number of rRNAs": "2", "Number of tRNAs": "56", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 79.6898, "matched_fragments": 577, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas hamiltonii", "strain": "strain=KCTC 22154", "accession": "GCA_014651775.1", "taxid": 502829, "species_taxid": 502829, "relation_to_type": "type", "validated": true, "ani": 79.6298, "matched_fragments": 500, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas stevensii", "strain": "strain=S18214", "accession": "GCA_000275725.1", "taxid": 502821, "species_taxid": 502821, "relation_to_type": "type", "validated": true, "ani": 79.4853, "matched_fragments": 507, "total_fragments": 1305, "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": 79.3176, "matched_fragments": 456, "total_fragments": 1305, "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": 79.2803, "matched_fragments": 421, "total_fragments": 1305, "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": 79.2625, "matched_fragments": 396, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas saccharevitans", "strain": "strain=CGMCC 1.6493", "accession": "GCA_900116405.1", "taxid": 416872, "species_taxid": 416872, "relation_to_type": "type", "validated": true, "ani": 79.2131, "matched_fragments": 409, "total_fragments": 1305, "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": 79.1394, "matched_fragments": 444, "total_fragments": 1305, "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": 79.1282, "matched_fragments": 397, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lactosivorans", "strain": "strain=KCTC 52281", "accession": "GCA_003254665.1", "taxid": 2185141, "species_taxid": 2185141, "relation_to_type": "type", "validated": true, "ani": 79.0968, "matched_fragments": 456, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas piezotolerans", "strain": "strain=NBT06E8", "accession": "GCA_012427705.1", "taxid": 2609667, "species_taxid": 2609667, "relation_to_type": "type", "validated": true, "ani": 79.0924, "matched_fragments": 437, "total_fragments": 1305, "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": 79.0423, "matched_fragments": 393, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas piezotolerans", "strain": "strain=NBT06E8", "accession": "GCA_009660035.1", "taxid": 2609667, "species_taxid": 2609667, "relation_to_type": "type", "validated": true, "ani": 79.0331, "matched_fragments": 437, "total_fragments": 1305, "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": 79.0151, "matched_fragments": 451, "total_fragments": 1305, "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": 78.9393, "matched_fragments": 456, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas bachuensis", "strain": "strain=DX6", "accession": "GCA_011742165.1", "taxid": 2717286, "species_taxid": 2717286, "relation_to_type": "type", "validated": true, "ani": 78.848, "matched_fragments": 407, "total_fragments": 1305, "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": 78.8411, "matched_fragments": 429, "total_fragments": 1305, "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": 78.758, "matched_fragments": 357, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas zhangzhouensis", "strain": "strain=MCCC 1A11036", "accession": "GCA_021404465.1", "taxid": 2733481, "species_taxid": 2733481, "relation_to_type": "type", "validated": true, "ani": 78.7292, "matched_fragments": 410, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas icarae", "strain": "strain=D1-1", "accession": "GCA_009901955.1", "taxid": 2691040, "species_taxid": 2691040, "relation_to_type": "type", "validated": true, "ani": 78.7283, "matched_fragments": 349, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas subglaciescola", "strain": "strain=ACAM 12", "accession": "GCA_900142895.1", "taxid": 29571, "species_taxid": 29571, "relation_to_type": "type", "validated": true, "ani": 78.6433, "matched_fragments": 360, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas kenyensis", "strain": "strain=DSM 17331", "accession": "GCA_013697085.1", "taxid": 321266, "species_taxid": 321266, "relation_to_type": "type", "validated": true, "ani": 78.6174, "matched_fragments": 408, "total_fragments": 1305, "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": 78.6024, "matched_fragments": 406, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas halodenitrificans", "strain": "strain=DSM 735", "accession": "GCA_000620045.1", "taxid": 28252, "species_taxid": 28252, "relation_to_type": "type", "validated": true, "ani": 78.321, "matched_fragments": 340, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lutea", "strain": "strain=DSM 23508", "accession": "GCA_000378505.1", "taxid": 453962, "species_taxid": 453962, "relation_to_type": "type", "validated": true, "ani": 77.7972, "matched_fragments": 240, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter lipolyticus", "strain": "strain=SM19", "accession": "GCA_000397065.2", "taxid": 209639, "species_taxid": 209639, "relation_to_type": "type", "validated": true, "ani": 76.7045, "matched_fragments": 69, "total_fragments": 1305, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003002925.1", "gtdb_species": "s__Halomonas songnenensis", "ani": 79.6898, "matched_fragments": 577, "total_fragments": 1305, "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_014651775.1", "gtdb_species": "s__Halomonas hamiltonii", "ani": 79.6302, "matched_fragments": 500, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.843, "mean_intra_species_ani": "98.09", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.88", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_000275725.1", "gtdb_species": "s__Halomonas stevensii", "ani": 79.4856, "matched_fragments": 507, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.843, "mean_intra_species_ani": "97.33", "min_intra_species_ani": "97.21", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.83", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCF_003056305.1", "gtdb_species": "s__Halomonas denitrificans", "ani": 79.3335, "matched_fragments": 455, "total_fragments": 1305, "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_000265245.1", "gtdb_species": "s__Halomonas smyrnensis", "ani": 79.2685, "matched_fragments": 395, "total_fragments": 1305, "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_009846525.1", "gtdb_species": "s__Halomonas sp002696125", "ani": 79.2673, "matched_fragments": 417, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "98.53", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_011742915.1", "gtdb_species": "s__Halomonas desiderata", "ani": 79.2539, "matched_fragments": 439, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.30", "min_intra_species_ani": "98.24", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_007989465.1", "gtdb_species": "s__Halomonas halophila", "ani": 79.2463, "matched_fragments": 424, "total_fragments": 1305, "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_900116405.1", "gtdb_species": "s__Halomonas saccharevitans", "ani": 79.2007, "matched_fragments": 411, "total_fragments": 1305, "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_015992245.1", "gtdb_species": "s__Halomonas sp015992245", "ani": 79.1094, "matched_fragments": 452, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "99.35", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003254665.1", "gtdb_species": "s__Halomonas lactosivorans", "ani": 79.106, "matched_fragments": 456, "total_fragments": 1305, "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": 79.1053, "matched_fragments": 399, "total_fragments": 1305, "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_012427705.1", "gtdb_species": "s__Halomonas piezotolerans", "ani": 79.1029, "matched_fragments": 436, "total_fragments": 1305, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.35", "min_intra_species_ani": "98.70", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003202205.1", "gtdb_species": "s__Halomonas sp003202205", "ani": 79.048, "matched_fragments": 427, "total_fragments": 1305, "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_004363555.1", "gtdb_species": "s__Halomonas ventosae", "ani": 78.9887, "matched_fragments": 413, "total_fragments": 1305, "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": "GCA_018401555.1", "gtdb_species": "s__Halomonas sp018401555", "ani": 78.9488, "matched_fragments": 363, "total_fragments": 1305, "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_011742165.1", "gtdb_species": "s__Halomonas bachuensis", "ani": 78.8307, 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