{ "type": "genome", "identifier": "GCF_900142755.1", "organism": "Halomonas cupida", "title": "Halomonas cupida", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900142755.1", "bioproject": "PRJNA224116", "biosample": "SAMN05660971", "wgs_master": "FRCA00000000.1", "refseq_category": "reference genome", "taxid": "44933", "species_taxid": "44933", "organism_name": "Halomonas cupida", "infraspecific_name": "strain=DSM 4740", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/12/03", "asm_name": "IMG-taxon 2599185207 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900142755.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/142/755/GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4957973", "genome_size_ungapped": "4953058", "gc_percent": "59.500000", "replicon_count": "0", "scaffold_count": "31", "contig_count": "31", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900142755.1-RS_2024_12_09", "annotation_date": "2024-12-09", "total_gene_count": "4469", "protein_coding_gene_count": "4384", "non_coding_gene_count": "59", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-12-03", "dateModified": "2016-12-03", "datePublished": "2016-12-03", "_annotation": { "sample_count": 1, "sample_organism": [ "Halomonas cupida" ], "sample_taxid": [ "44933" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.393 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)": "4957973", "Number of Sequences": "31", "Longest Sequences (bp)": "958871", "N50 (bp)": "383301", "Gap Ratio (%)": "0.099133", "GCcontent (%)": "59.6", "Number of CDSs": "4353", "Average Protein Length": "328.4", "Coding Ratio (%)": "86.5", "Number of rRNAs": "2", "Number of tRNAs": "52", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas cupida", "strain": "strain=DSM 4740", "accession": "GCA_900142755.1", "taxid": 44933, "species_taxid": 44933, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1636, "total_fragments": 1636, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halomonas cupida", "strain": "strain=NBRC 102219", "accession": "GCA_007991155.1", "taxid": 44933, "species_taxid": 44933, "relation_to_type": "type", "validated": true, "ani": 99.8723, "matched_fragments": 1509, "total_fragments": 1636, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Halomonas huangheensis", "strain": "strain=BJGMM-B45", "accession": "GCA_001431725.1", "taxid": 1178482, "species_taxid": 1178482, "relation_to_type": "type", "validated": true, "ani": 81.9666, "matched_fragments": 1076, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas huangheensis", "strain": "strain=BJGMM-B45", "accession": "GCA_000470745.1", "taxid": 1178482, "species_taxid": 1178482, "relation_to_type": "type", "validated": true, "ani": 81.8945, "matched_fragments": 1073, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas litopenaei", "strain": "strain=SYSU ZJ2214", "accession": "GCA_003045775.1", "taxid": 2109328, "species_taxid": 2109328, "relation_to_type": "type", "validated": true, "ani": 79.8546, "matched_fragments": 711, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas borealis", "strain": "strain=ATF 5.2", "accession": "GCA_004798905.1", "taxid": 2508710, "species_taxid": 2508710, "relation_to_type": "type", "validated": true, "ani": 79.2659, "matched_fragments": 474, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lysinitropha", "strain": "strain=3(2)", "accession": "GCA_902500215.1", "taxid": 2607506, "species_taxid": 2607506, "relation_to_type": "type", "validated": true, "ani": 78.8922, "matched_fragments": 428, "total_fragments": 1636, "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": 78.8122, "matched_fragments": 452, "total_fragments": 1636, "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": 78.7967, "matched_fragments": 470, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas saliphila", "strain": "strain=LCB169", "accession": "GCA_002930105.1", "taxid": 1848458, "species_taxid": 1848458, "relation_to_type": "type", "validated": true, "ani": 78.6167, "matched_fragments": 438, "total_fragments": 1636, "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": 78.6066, "matched_fragments": 454, "total_fragments": 1636, "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": 78.5619, "matched_fragments": 467, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yangia pacifica", "strain": "strain=CGMCC 1.3455", "accession": "GCA_900100725.1", "taxid": 311180, "species_taxid": 311180, "relation_to_type": "suspected-type", "validated": true, "ani": 75.5435, "matched_fragments": 58, "total_fragments": 1636, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yangia 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Halomonas", "cupida" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }