{ "type": "genome", "identifier": "GCF_025370095.1", "organism": "Sphingomonas alpina", "title": "Sphingomonas alpina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_025370095.1", "bioproject": "PRJNA224116", "biosample": "SAMN30309222", "wgs_master": "JANQBJ000000000.1", "refseq_category": "reference genome", "taxid": "653931", "species_taxid": "653931", "organism_name": "Sphingomonas alpina", "infraspecific_name": "strain=DSM 22537", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/09/22", "asm_name": "ASM2537009v1", "asm_submitter": "University of Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_025370095.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/025/370/095/GCF_025370095.1_ASM2537009v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5195245", "genome_size_ungapped": "5195245", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_025370095.1-RS_2024_10_11", "annotation_date": "2024-10-11", "total_gene_count": "4841", "protein_coding_gene_count": "4763", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-09-22", "dateModified": "2022-09-22", "datePublished": "2022-09-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas alpina" ], "sample_taxid": [ "653931" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Austria" ], "sample_host_location_id": [], "data_size": "1.433 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)": "5195245", "Number of Sequences": "20", "Longest Sequences (bp)": "1259247", "N50 (bp)": "758285", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "64.0", "Number of CDSs": "4795", "Average Protein Length": "325.2", "Coding Ratio (%)": "90.0", "Number of rRNAs": "3", "Number of tRNAs": "54", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas alpina", "strain": "strain=DSM 22537", "accession": "GCA_025370095.1", "taxid": 653931, "species_taxid": 653931, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1719, "total_fragments": 1722, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingomonas alpina", "strain": "strain=DSM 22537", "accession": "GCA_014490665.1", "taxid": 653931, "species_taxid": 653931, "relation_to_type": "type", "validated": true, "ani": 99.9912, "matched_fragments": 1722, "total_fragments": 1722, "ani_threshold": 95, "status": "conclusive" }, { "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": 81.339, "matched_fragments": 724, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas glacialis", "strain": "strain=CGMCC 1.8957", "accession": "GCA_014653575.1", "taxid": 658225, "species_taxid": 658225, "relation_to_type": "type", "validated": true, "ani": 80.1758, "matched_fragments": 652, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas aliaeris", "strain": "strain=DH-S5", "accession": "GCA_016743815.1", "taxid": 2759526, "species_taxid": 2759526, "relation_to_type": "type", "validated": true, "ani": 79.9638, "matched_fragments": 635, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas populi", "strain": "strain=3-7", "accession": "GCA_004208535.1", "taxid": 2484750, "species_taxid": 2484750, "relation_to_type": "type", "validated": true, "ani": 79.9124, "matched_fragments": 581, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas panacis", "strain": "strain=DCY99", "accession": "GCA_001717955.1", "taxid": 1560345, "species_taxid": 1560345, "relation_to_type": "type", "validated": true, "ani": 79.767, "matched_fragments": 591, "total_fragments": 1722, "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": 79.0646, "matched_fragments": 527, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas gilva", "strain": "strain=ZDH117", "accession": "GCA_003515075.1", "taxid": 2305907, "species_taxid": 2305907, "relation_to_type": "type", "validated": true, "ani": 78.9339, "matched_fragments": 569, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas koreensis", "strain": "strain=JSS26", "accession": "GCA_002797435.1", "taxid": 93064, "species_taxid": 93064, "relation_to_type": "type", "validated": true, "ani": 78.9226, "matched_fragments": 552, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas koreensis", "strain": "strain=NBRC 16723", "accession": "GCA_001598395.1", "taxid": 93064, "species_taxid": 93064, "relation_to_type": "type", "validated": true, "ani": 78.8941, "matched_fragments": 547, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas aracearum", "strain": "strain=WZY 27", "accession": "GCA_003345355.1", "taxid": 2283317, "species_taxid": 2283317, "relation_to_type": "type", "validated": true, "ani": 78.847, "matched_fragments": 521, "total_fragments": 1722, "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": 78.6964, "matched_fragments": 482, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014490665.1", "gtdb_species": "s__Sphingomonas alpina", "ani": 99.9912, "matched_fragments": 1722, "total_fragments": 1722, "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": "conclusive" }, { "accession": "GCF_000803065.1", "gtdb_species": "s__Sphingomonas sp000803065", "ani": 86.9625, "matched_fragments": 1326, "total_fragments": 1722, "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_014171475.1", "gtdb_species": "s__Sphingomonas alpina_A", "ani": 85.9467, "matched_fragments": 1113, "total_fragments": 1722, "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_001423845.1", "gtdb_species": "s__Sphingomonas sp001423845", "ani": 81.1221, "matched_fragments": 711, "total_fragments": 1722, "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_903884945.1", "gtdb_species": "s__Sphingomonas sp903884945", "ani": 80.5065, "matched_fragments": 754, "total_fragments": 1722, "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_000241485.1", "gtdb_species": "s__Sphingomonas sp000241485", "ani": 80.2868, "matched_fragments": 669, "total_fragments": 1722, "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_014653575.1", "gtdb_species": "s__Sphingomonas glacialis", "ani": 80.2072, "matched_fragments": 648, "total_fragments": 1722, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.17", "min_intra_species_ani": "97.17", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.81", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_016743815.1", "gtdb_species": "s__Sphingomonas sp016743815", "ani": 79.9848, "matched_fragments": 633, "total_fragments": 1722, "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": 79.8329, "matched_fragments": 561, "total_fragments": 1722, "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_001717955.1", "gtdb_species": "s__Sphingomonas panacis", "ani": 79.7687, "matched_fragments": 587, "total_fragments": 1722, "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_009789535.1", "gtdb_species": "s__Sphingomonas carotinifaciens", "ani": 79.0143, "matched_fragments": 523, "total_fragments": 1722, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.06", "min_intra_species_ani": "97.19", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.90", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002797435.1", "gtdb_species": "s__Sphingomonas koreensis", "ani": 78.9223, "matched_fragments": 553, "total_fragments": 1722, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.13", "min_intra_species_ani": "98.00", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.86", "num_clustered_genomes": 72, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.155, "cell_length": 0.079, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 28.407, "optimum_ph": 7.5, "genome_size": 4164406.103, "gc_content": 66.116, "coding_genes": 4592.69, "rRNA16S_genes": 2.285, "tRNA_genes": 51.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "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": [ "Sphingomonas", "alpina" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }