{ "type": "genome", "identifier": "GCF_012274265.1", "organism": "Sphingopyxis microcysteis", "title": "Sphingopyxis microcysteis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Zhejiang Ocean University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_012274265.1", "bioproject": "PRJNA224116", "biosample": "SAMN14342411", "wgs_master": "JAANYY000000000.1", "refseq_category": "reference genome", "taxid": "2484145", "species_taxid": "2484145", "organism_name": "Sphingopyxis microcysteis", "infraspecific_name": "strain=Z10-6", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/04/13", "asm_name": "ASM1227426v1", "asm_submitter": "Zhejiang Ocean University", "gbrs_paired_asm": "GCA_012274265.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/012/274/265/GCF_012274265.1_ASM1227426v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3463217", "genome_size_ungapped": "3463217", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "10", "contig_count": "10", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_012274265.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3303", "protein_coding_gene_count": "3225", "non_coding_gene_count": "52", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-04-13", "dateModified": "2020-04-13", "datePublished": "2020-04-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingopyxis microcysteis" ], "sample_taxid": [ "2484145" ], "sample_host_organism": [ "Dinoflagellate" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: the East China Sea" ], "sample_host_location_id": [], "data_size": "0.948 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "3463217", "Number of Sequences": "10", "Longest Sequences (bp)": "1648809", "N50 (bp)": "754638", "Gap Ratio (%)": "0.000260", "GCcontent (%)": "64.8", "Number of CDSs": "3266", "Average Protein Length": "319.6", "Coding Ratio (%)": "90.4", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingopyxis microcysteis", "strain": "strain=Z10-6", "accession": "GCA_012274265.1", "taxid": 2484145, "species_taxid": 2484145, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1148, "total_fragments": 1149, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingopyxis bauzanensis", "strain": "strain=DSM 22271", "accession": "GCA_002205675.1", "taxid": 651663, "species_taxid": 651663, "relation_to_type": "type", "validated": true, "ani": 87.0148, "matched_fragments": 874, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis bauzanensis", "strain": "strain=CGMCC 1.8959", "accession": "GCA_014645635.1", "taxid": 651663, "species_taxid": 651663, "relation_to_type": "type", "validated": true, "ani": 86.9791, "matched_fragments": 872, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis solisilvae", "strain": "strain=R366", "accession": "GCA_015475875.1", "taxid": 1886788, "species_taxid": 1886788, "relation_to_type": "type", "validated": true, "ani": 86.8592, "matched_fragments": 837, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis italica", "strain": "strain=DSM 25229", "accession": "GCA_011926545.1", "taxid": 1129133, "species_taxid": 1129133, "relation_to_type": "type", "validated": true, "ani": 85.4968, "matched_fragments": 849, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis fribergensis", "strain": "strain=Kp5.2", "accession": "GCA_000803645.1", "taxid": 1515612, "species_taxid": 1515612, "relation_to_type": "type", "validated": true, "ani": 85.3179, "matched_fragments": 865, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis alaskensis", "strain": "strain=RB2256", "accession": "GCA_000013985.1", "taxid": 117207, "species_taxid": 117207, "relation_to_type": "type", "validated": true, "ani": 84.8118, "matched_fragments": 791, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis macrogoltabida", "strain": "strain=203", "accession": "GCA_001314325.1", "taxid": 33050, "species_taxid": 33050, "relation_to_type": "type", "validated": true, "ani": 84.6669, "matched_fragments": 832, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis panaciterrae", "strain": "strain=DSM 27164", "accession": "GCA_011762125.1", "taxid": 363841, "species_taxid": 363841, "relation_to_type": "type", "validated": true, "ani": 84.4676, "matched_fragments": 840, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis soli", "strain": "strain=BL03", "accession": "GCA_018682675.1", "taxid": 592051, "species_taxid": 592051, "relation_to_type": "type", "validated": true, "ani": 84.2426, "matched_fragments": 755, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis terrae subsp. ummariensis", "strain": "strain=DSM 24316", "accession": "GCA_002374275.1", "taxid": 429001, "species_taxid": 33052, "relation_to_type": "type", "validated": true, "ani": 83.4509, "matched_fragments": 784, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium percolationis", "strain": "strain=c1", "accession": "GCA_020179425.1", "taxid": 2871811, "species_taxid": 2871811, "relation_to_type": "type", "validated": true, "ani": 78.3333, "matched_fragments": 332, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas cavernae", "strain": "strain=K2R01-6", "accession": "GCA_003590775.1", "taxid": 2320861, "species_taxid": 2320861, "relation_to_type": "type", "validated": true, "ani": 78.2759, "matched_fragments": 371, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium huizhouense", "strain": "strain=c7", "accession": "GCA_020179475.1", "taxid": 2866625, "species_taxid": 2866625, "relation_to_type": "type", "validated": true, "ani": 78.2121, "matched_fragments": 344, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pelagerythrobacter rhizovicinus", "strain": "strain=AY-3R", "accession": "GCA_004135625.1", "taxid": 2268576, "species_taxid": 2268576, "relation_to_type": "type", "validated": true, "ani": 77.7553, "matched_fragments": 265, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Qipengyuania polymorpha", "strain": "strain=1NDH17", "accession": "GCA_019711435.1", "taxid": 2867234, "species_taxid": 2867234, "relation_to_type": "type", "validated": true, "ani": 77.6063, "matched_fragments": 240, "total_fragments": 1149, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_012274265.1", "gtdb_species": "s__Sphingopyxis microcysteis", "ani": 100.0, "matched_fragments": 1148, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.26", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_005503695.1", "gtdb_species": "s__Sphingopyxis sp003609815", "ani": 94.9635, "matched_fragments": 968, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.15", "min_intra_species_ani": "97.15", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.90", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002454115.1", "gtdb_species": "s__Sphingopyxis sp002454115", "ani": 87.4754, "matched_fragments": 891, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_005502465.1", "gtdb_species": "s__Sphingopyxis sp005502465", "ani": 87.4535, "matched_fragments": 900, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_016463225.1", "gtdb_species": "s__Sphingopyxis sp016463225", "ani": 87.4034, "matched_fragments": 869, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_002205675.1", "gtdb_species": "s__Sphingopyxis bauzanensis", "ani": 87.0148, "matched_fragments": 874, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_015475875.1", "gtdb_species": "s__Sphingopyxis solisilvae", "ani": 86.8592, "matched_fragments": 837, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.45", "min_intra_species_ani": "96.45", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000756375.1", "gtdb_species": "s__Sphingopyxis sp000756375", "ani": 85.8112, "matched_fragments": 857, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_005503215.1", "gtdb_species": "s__Sphingopyxis sp005503215", "ani": 85.717, "matched_fragments": 879, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.20", "min_intra_species_ani": "99.20", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_900078365.1", "gtdb_species": "s__Sphingopyxis sp900078365", "ani": 85.5087, "matched_fragments": 858, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_011926545.1", "gtdb_species": "s__Sphingopyxis italica", "ani": 85.4968, "matched_fragments": 849, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_000756385.1", "gtdb_species": "s__Sphingopyxis sp000756385", "ani": 85.4169, "matched_fragments": 839, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_013410105.1", "gtdb_species": "s__Sphingopyxis sp013410105", "ani": 85.1547, "matched_fragments": 851, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "99.44", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900108295.1", "gtdb_species": "s__Sphingopyxis sp900108295", "ani": 84.865, "matched_fragments": 850, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_017745175.1", "gtdb_species": "s__Sphingopyxis sp017745175", "ani": 84.6268, "matched_fragments": 811, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_016463645.1", "gtdb_species": "s__Sphingopyxis sp016463645", "ani": 84.5902, "matched_fragments": 737, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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_001047015.1", "gtdb_species": "s__Sphingopyxis sp001047015", "ani": 84.5148, "matched_fragments": 867, "total_fragments": 1149, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "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": -0.437, "cell_length": -0.047, "doubling_h": 0.518, "growth_tmp": 28.125, "optimum_tmp": 26.35, "optimum_ph": 7.083, "genome_size": 4171312.217, "gc_content": 63.768, "coding_genes": 4202.933, "rRNA16S_genes": 1.0, "tRNA_genes": 47.4, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.818, "range_salinity": null, "facultative_respiration": 0.066, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.933, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.909, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.09, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Sphingopyxis", "microcysteis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }