{ "type": "genome", "identifier": "GCF_019351405.1", "organism": "Stakelama flava", "title": "Stakelama flava", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Life sciences Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019351405.1", "bioproject": "PRJNA224116", "biosample": "SAMN20296684", "wgs_master": "JAHWZX000000000.1", "refseq_category": "reference genome", "taxid": "2860338", "species_taxid": "2860338", "organism_name": "Stakelama flava", "infraspecific_name": "strain=CBK3Z-3", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/07/26", "asm_name": "ASM1935140v1", "asm_submitter": "Life sciences Institute", "gbrs_paired_asm": "GCA_019351405.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/351/405/GCF_019351405.1_ASM1935140v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3387040", "genome_size_ungapped": "3387020", "gc_percent": "62.500000", "replicon_count": "0", "scaffold_count": "34", "contig_count": "34", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019351405.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "3266", "protein_coding_gene_count": "3145", "non_coding_gene_count": "53", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-07-26", "dateModified": "2021-07-26", "datePublished": "2021-07-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Stakelama flava" ], "sample_taxid": [ "2860338" ], "sample_host_organism": [ "plant" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Guangxi" ], "sample_host_location_id": [], "data_size": "0.939 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)": "3387040", "Number of Sequences": "34", "Longest Sequences (bp)": "435337", "N50 (bp)": "182725", "Gap Ratio (%)": "0.000590", "GCcontent (%)": "62.6", "Number of CDSs": "3190", "Average Protein Length": "321.5", "Coding Ratio (%)": "90.8", "Number of rRNAs": "3", "Number of tRNAs": "46", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Stakelama flava", "strain": "strain=CBK3Z-3", "accession": "GCA_019351405.1", "taxid": 2860338, "species_taxid": 2860338, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1110, "total_fragments": 1113, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Stakelama pacifica", "strain": "strain=CGMCC 1.7294", "accession": "GCA_014645395.1", "taxid": 517720, "species_taxid": 517720, "relation_to_type": "type", "validated": true, "ani": 82.661, "matched_fragments": 732, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stakelama pacifica", "strain": "strain=DSM 25059", "accession": "GCA_004361835.1", "taxid": 517720, "species_taxid": 517720, "relation_to_type": "type", "validated": true, "ani": 82.6376, "matched_fragments": 734, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stakelama sediminis", "strain": "strain=DSM 27203", "accession": "GCA_014199335.1", "taxid": 463200, "species_taxid": 463200, "relation_to_type": "type", "validated": true, "ani": 79.8321, "matched_fragments": 501, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingosinithalassobacter tenebrarum", "strain": "strain=zrk23", "accession": "GCA_011057975.1", "taxid": 2711215, "species_taxid": 2711215, "relation_to_type": "type", "validated": true, "ani": 79.0914, "matched_fragments": 444, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingosinithalassobacter portus", "strain": "strain=FM6", "accession": "GCA_003171655.1", "taxid": 2676234, "species_taxid": 2676234, "relation_to_type": "type", "validated": true, "ani": 78.9756, "matched_fragments": 447, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas japonica", "strain": "strain=DSM 22753", "accession": "GCA_011762085.1", "taxid": 511662, "species_taxid": 511662, "relation_to_type": "type", "validated": true, "ani": 78.5276, "matched_fragments": 380, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hankookensis", "strain": "strain=KCTC 22579", "accession": "GCA_022664465.1", "taxid": 563996, "species_taxid": 563996, "relation_to_type": "type", "validated": true, "ani": 78.3725, "matched_fragments": 401, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas suaedae", "strain": "strain=XS-10", "accession": "GCA_007833215.1", "taxid": 2599297, "species_taxid": 2599297, "relation_to_type": "type", "validated": true, "ani": 78.3475, "matched_fragments": 432, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas baiyangensis", "strain": "strain=L-1-4 w-11", "accession": "GCA_005144715.1", "taxid": 2572576, "species_taxid": 2572576, "relation_to_type": "type", "validated": true, "ani": 78.2988, "matched_fragments": 378, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas panni", "strain": "strain=DSM 15761", "accession": "GCA_022664435.1", "taxid": 237612, "species_taxid": 237612, "relation_to_type": "type", "validated": true, "ani": 78.2163, "matched_fragments": 393, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas trueperi", "strain": "strain=DSM 7225", "accession": "GCA_011927635.1", "taxid": 53317, "species_taxid": 53317, "relation_to_type": "type", "validated": true, "ani": 78.1297, "matched_fragments": 403, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas naasensis", "strain": "strain=DSM 100060", "accession": "GCA_011762145.1", "taxid": 1344951, "species_taxid": 1344951, "relation_to_type": "type", "validated": true, "ani": 77.9465, "matched_fragments": 406, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas colocasiae", "strain": "strain=JCM 31229", "accession": "GCA_019880585.1", "taxid": 1848973, "species_taxid": 1848973, "relation_to_type": "type", "validated": true, "ani": 77.9005, "matched_fragments": 386, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hylomeconis", "strain": "strain=CCTCC AB 2013304", "accession": "GCA_025370105.1", "taxid": 1395958, "species_taxid": 1395958, "relation_to_type": "type", "validated": true, "ani": 77.7695, "matched_fragments": 392, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania proteolytica", "strain": "strain=6B39", "accession": "GCA_019711565.1", "taxid": 2867239, "species_taxid": 2867239, "relation_to_type": "type", "validated": true, "ani": 77.2845, "matched_fragments": 179, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas folli", "strain": "strain=RHCKR7", "accession": "GCA_019429525.1", "taxid": 2862497, "species_taxid": 2862497, "relation_to_type": "type", "validated": true, "ani": 77.2663, "matched_fragments": 302, "total_fragments": 1113, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004361835.1", "gtdb_species": "s__Sphingomonas pacifica", "ani": 82.6265, "matched_fragments": 735, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.75", "min_intra_species_ani": "97.51", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.77", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCA_018122655.1", "gtdb_species": "s__Sphingomonas sp018122655", "ani": 79.9441, "matched_fragments": 522, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_014199335.1", "gtdb_species": "s__Sphingomonas sediminis", "ani": 79.8444, "matched_fragments": 499, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_003171655.1", "gtdb_species": "s__Sphingomonas portus", "ani": 78.9705, "matched_fragments": 447, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_001555965.1", "gtdb_species": "s__Sphingomonas sp001555965", "ani": 78.7868, "matched_fragments": 419, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.33", "min_intra_species_ani": "97.92", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.78", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_014334115.1", "gtdb_species": "s__Sphingomonas sp014334115", "ani": 78.49, "matched_fragments": 411, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_902826325.1", "gtdb_species": "s__Sphingomonas sp902826325", "ani": 78.4791, "matched_fragments": 346, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.74", "min_intra_species_ani": "97.74", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.84", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_003240755.1", "gtdb_species": "s__Sphingomonas hengshuiensis_A", "ani": 78.4424, "matched_fragments": 390, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_006346325.1", "gtdb_species": "s__Sphingomonas japonica", "ani": 78.4128, "matched_fragments": 386, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013409985.1", "gtdb_species": "s__Sphingomonas melonis_A", "ani": 78.1814, "matched_fragments": 364, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_002127225.1", "gtdb_species": "s__Sphingomonas sp002127225", "ani": 78.107, "matched_fragments": 393, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_018240825.1", "gtdb_species": "s__Sphingomonas sp018240825", "ani": 78.0485, "matched_fragments": 218, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_011761945.1", "gtdb_species": "s__Sphingomonas leidyi", "ani": 77.9714, "matched_fragments": 399, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.87", "min_intra_species_ani": "98.83", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002197685.1", "gtdb_species": "s__Sphingomonas dokdonensis", "ani": 77.8941, "matched_fragments": 297, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_002002925.1", "gtdb_species": "s__Sphingomonas sp002002925", "ani": 77.856, "matched_fragments": 379, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_900103265.1", "gtdb_species": "s__Sphingomonas sp900103265", "ani": 77.8494, "matched_fragments": 356, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_003345355.1", "gtdb_species": "s__Sphingomonas sp003345355", "ani": 77.7821, "matched_fragments": 348, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_004173185.1", "gtdb_species": "s__Sphingomonas sp004173185", "ani": 77.4247, "matched_fragments": 325, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "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_004564275.1", "gtdb_species": "s__Allosphingosinicella parva", "ani": 77.0924, "matched_fragments": 231, "total_fragments": 1113, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella", "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": -0.302, "cell_length": 0.176, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 29.0, "optimum_ph": 7.0, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.5, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Stakelama", "flava" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }