{ "type": "genome", "identifier": "GCF_900111305.1", "organism": "Vreelandella subterranea", "title": "Vreelandella subterranea", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900111305.1", "bioproject": "PRJNA224116", "biosample": "SAMN04487958", "wgs_master": "FOGS00000000.1", "refseq_category": "reference genome", "taxid": "416874", "species_taxid": "416874", "organism_name": "Vreelandella subterranea", "infraspecific_name": "strain=CGMCC 1.6495", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2617270764 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900111305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/111/305/GCF_900111305.1_IMG-taxon_2617270764_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": "3734199", "genome_size_ungapped": "3732405", "gc_percent": "58.000000", "replicon_count": "0", "scaffold_count": "26", "contig_count": "26", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900111305.1-RS_2024_04_07", "annotation_date": "2024-04-07", "total_gene_count": "3586", "protein_coding_gene_count": "3492", "non_coding_gene_count": "70", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Vreelandella subterranea" ], "sample_taxid": [ "416874" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.060 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)": "3734199", "Number of Sequences": "26", "Longest Sequences (bp)": "626146", "N50 (bp)": "261622", "Gap Ratio (%)": "0.048042", "GCcontent (%)": "58.0", "Number of CDSs": "3528", "Average Protein Length": "317.7", "Coding Ratio (%)": "90.0", "Number of rRNAs": "6", "Number of tRNAs": "50", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halomonas arcis", "strain": "strain=CGMCC 1.6494", "accession": "GCA_900103865.1", "taxid": 416873, "species_taxid": 416873, "relation_to_type": "type", "validated": true, "ani": 81.885, "matched_fragments": 822, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas titanicae", "strain": "strain=BH1", "accession": "GCA_000336575.1", "taxid": 664683, "species_taxid": 664683, "relation_to_type": "type", "validated": true, "ani": 79.9256, "matched_fragments": 611, "total_fragments": 1233, "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": 79.8893, "matched_fragments": 575, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aquamarina", "strain": "strain=558", "accession": "GCA_900110265.1", "taxid": 77097, "species_taxid": 77097, "relation_to_type": "type", "validated": true, "ani": 79.8712, "matched_fragments": 480, "total_fragments": 1233, "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": 79.8133, "matched_fragments": 556, "total_fragments": 1233, "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": 79.775, "matched_fragments": 537, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas meridiana", "strain": "strain=ACAM 246", "accession": "GCA_900129255.1", "taxid": 29570, "species_taxid": 29570, "relation_to_type": "type", "validated": true, "ani": 79.7517, "matched_fragments": 489, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas meridiana", "strain": "strain=NBRC 15608", "accession": "GCA_006540125.1", "taxid": 29570, "species_taxid": 29570, "relation_to_type": "type", "validated": true, "ani": 79.6905, "matched_fragments": 469, "total_fragments": 1233, "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": 79.6749, "matched_fragments": 492, "total_fragments": 1233, "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": 79.5432, "matched_fragments": 492, "total_fragments": 1233, "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": 79.4924, "matched_fragments": 509, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lutescens", "strain": "strain=CGMCC 1.15122", "accession": "GCA_014640815.1", "taxid": 1602943, "species_taxid": 1602943, "relation_to_type": "type", "validated": true, "ani": 79.428, "matched_fragments": 482, "total_fragments": 1233, "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": 79.1491, "matched_fragments": 417, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas massiliensis", "strain": "strain=Marseille-P2426", "accession": "GCA_900155385.1", "taxid": 1816686, "species_taxid": 1816686, "relation_to_type": "type", "validated": true, "ani": 78.9993, "matched_fragments": 373, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas nanhaiensis", "strain": "strain=JCM 18142", "accession": "GCA_003990185.1", "taxid": 1258546, "species_taxid": 1258546, "relation_to_type": "type", "validated": true, "ani": 78.9261, "matched_fragments": 429, "total_fragments": 1233, "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": 78.5853, "matched_fragments": 337, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas shengliensis", "strain": "strain=CGMCC 1.6444", "accession": "GCA_900104135.1", "taxid": 419597, "species_taxid": 419597, "relation_to_type": "type", "validated": true, "ani": 78.3556, "matched_fragments": 339, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas taeanensis", "strain": "strain=BH539", "accession": "GCA_900100755.1", "taxid": 284577, "species_taxid": 284577, "relation_to_type": "type", "validated": true, "ani": 78.2301, "matched_fragments": 287, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas stenophila", "strain": "strain=CECT 7744", "accession": "GCA_014192275.1", "taxid": 795312, "species_taxid": 795312, "relation_to_type": "type", "validated": true, "ani": 78.1929, "matched_fragments": 357, "total_fragments": 1233, "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": 78.1803, "matched_fragments": 360, "total_fragments": 1233, "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": 78.1027, "matched_fragments": 317, "total_fragments": 1233, "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": 78.0897, "matched_fragments": 323, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas ventosae", "strain": "strain=CECT 5797", "accession": "GCA_004363555.1", "taxid": 229007, "species_taxid": 229007, "relation_to_type": "type", "validated": true, "ani": 78.0634, "matched_fragments": 355, "total_fragments": 1233, "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": 78.0595, "matched_fragments": 313, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas pellis", "strain": "strain=L5", "accession": "GCA_008297955.1", "taxid": 2606936, "species_taxid": 2606936, "relation_to_type": "type", "validated": true, "ani": 77.9732, "matched_fragments": 297, "total_fragments": 1233, "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": 77.9355, "matched_fragments": 310, "total_fragments": 1233, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900111305.1", "gtdb_species": "s__Halomonas subterranea", "ani": 100.0, "matched_fragments": 1232, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.10", "min_intra_species_ani": "95.10", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_015767635.1", "gtdb_species": "s__Halomonas sp002119345", "ani": 91.4881, "matched_fragments": 1029, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014263395.1", "gtdb_species": "s__Halomonas sp014263395", "ani": 89.7762, "matched_fragments": 1000, "total_fragments": 1233, "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_000686925.1", "gtdb_species": "s__Halomonas sp000686925", "ani": 84.0698, "matched_fragments": 905, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900086985.1", "gtdb_species": "s__Halomonas sp900086985", "ani": 83.5767, "matched_fragments": 902, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.32", "min_intra_species_ani": "98.66", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900103865.1", "gtdb_species": "s__Halomonas arcis", "ani": 81.8929, "matched_fragments": 821, "total_fragments": 1233, "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": "GCA_001507855.1", "gtdb_species": "s__Halomonas sp001507855", "ani": 79.6016, "matched_fragments": 442, "total_fragments": 1233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003002925.1", "gtdb_species": "s__Halomonas songnenensis", "ani": 79.4826, "matched_fragments": 510, "total_fragments": 1233, "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Vreelandella", "subterranea" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }