{ "type": "genome", "identifier": "GCF_014653575.1", "organism": "Sphingomonas glacialis", "title": "Sphingomonas glacialis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014653575.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245162", "wgs_master": "BNAQ00000000.1", "refseq_category": "reference genome", "taxid": "658225", "species_taxid": "658225", "organism_name": "Sphingomonas glacialis", "infraspecific_name": "strain=CGMCC 1.8957", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1465357v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014653575.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/653/575/GCF_014653575.1_ASM1465357v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4470563", "genome_size_ungapped": "4470161", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "58", "contig_count": "58", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014653575.1-RS_2024_08_02", "annotation_date": "2024-08-02", "total_gene_count": "4266", "protein_coding_gene_count": "4142", "non_coding_gene_count": "53", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas glacialis" ], "sample_taxid": [ "658225" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.225 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4470563", "Number of Sequences": "58", "Longest Sequences (bp)": "1391625", "N50 (bp)": "863377", "Gap Ratio (%)": "0.008992", "GCcontent (%)": "65.7", "Number of CDSs": "4238", "Average Protein Length": "313.4", "Coding Ratio (%)": "89.1", "Number of rRNAs": "3", "Number of tRNAs": "49", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1469, "total_fragments": 1469, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Sphingomonas echinoides", "strain": "strain=ATCC 14820", "accession": "GCA_000241465.1", "taxid": 59803, "species_taxid": 59803, "relation_to_type": "type", "validated": true, "ani": 83.1327, "matched_fragments": 816, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas psychrolutea", "strain": "strain=CGMCC 1.10106", "accession": "GCA_014636175.1", "taxid": 1259676, "species_taxid": 1259676, "relation_to_type": "type", "validated": true, "ani": 82.8876, "matched_fragments": 796, "total_fragments": 1469, "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": 81.5021, "matched_fragments": 710, "total_fragments": 1469, "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": 81.1909, "matched_fragments": 696, "total_fragments": 1469, "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": 80.9414, "matched_fragments": 705, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas alpina", "strain": "strain=DSM 22537", "accession": "GCA_014490665.1", "taxid": 653931, "species_taxid": 653931, "relation_to_type": "type", "validated": true, "ani": 80.1401, "matched_fragments": 651, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas alpina", "strain": "strain=DSM 22537", "accession": "GCA_025370095.1", "taxid": 653931, "species_taxid": 653931, "relation_to_type": "type", "validated": true, "ani": 80.1268, "matched_fragments": 647, "total_fragments": 1469, "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": 79.9324, "matched_fragments": 616, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas azotifigens", "strain": "strain=NBRC 15497", "accession": "GCA_002091475.1", "taxid": 330920, "species_taxid": 330920, "relation_to_type": "type", "validated": true, "ani": 79.3241, "matched_fragments": 608, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas citri", "strain": "strain=RRHST34", "accession": "GCA_019429485.1", "taxid": 2862499, "species_taxid": 2862499, "relation_to_type": "type", "validated": true, "ani": 79.2989, "matched_fragments": 620, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas yunnanensis", "strain": "strain=YIM 3", "accession": "GCA_019898765.1", "taxid": 310400, "species_taxid": 310400, "relation_to_type": "type", "validated": true, "ani": 79.2789, "matched_fragments": 617, "total_fragments": 1469, "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": 79.2147, "matched_fragments": 621, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas kyeonggiensis", "strain": "strain=DSM 101806", "accession": "GCA_014196745.1", "taxid": 1268553, "species_taxid": 1268553, "relation_to_type": "type", "validated": true, "ani": 79.1614, "matched_fragments": 641, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas desiccabilis", "strain": "strain=DSM 16792", "accession": "GCA_014196135.1", "taxid": 429134, "species_taxid": 429134, "relation_to_type": "type", "validated": true, "ani": 79.0538, "matched_fragments": 475, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas desiccabilis", "strain": "strain=CP1D", "accession": "GCA_004135605.1", "taxid": 429134, "species_taxid": 429134, "relation_to_type": "type", "validated": true, "ani": 79.0134, "matched_fragments": 477, "total_fragments": 1469, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 95.83, "contamination": 4.17, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_014653575.1", "gtdb_species": "s__Sphingomonas glacialis", "ani": 100.0, "matched_fragments": 1469, "total_fragments": 1469, "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": "conclusive" }, { "accession": "GCF_006439055.1", "gtdb_species": "s__Sphingomonas glacialis_A", "ani": 90.3143, "matched_fragments": 1064, "total_fragments": 1469, "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": 89.0055, "matched_fragments": 998, "total_fragments": 1469, "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_000251145.1", "gtdb_species": "s__Sphingomonas sp000251145", "ani": 83.4413, "matched_fragments": 873, "total_fragments": 1469, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.28", "min_intra_species_ani": "96.28", "mean_intra_species_af": "0.82", "min_intra_species_af": "0.82", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000241465.1", "gtdb_species": "s__Sphingomonas echinoides", "ani": 83.1119, "matched_fragments": 818, "total_fragments": 1469, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.65", "min_intra_species_ani": "96.65", "mean_intra_species_af": "0.85", "min_intra_species_af": "0.85", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013374095.1", "gtdb_species": "s__Sphingomonas sp013374095", "ani": 82.8757, "matched_fragments": 775, "total_fragments": 1469, "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_014636175.1", "gtdb_species": "s__Sphingomonas psychrolutea", "ani": 82.8695, "matched_fragments": 798, "total_fragments": 1469, "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_000797515.1", "gtdb_species": "s__Sphingomonas sp000797515", "ani": 82.8072, "matched_fragments": 743, "total_fragments": 1469, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "97.12", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.75", "num_clustered_genomes": 5, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.302, "cell_length": -0.097, "doubling_h": null, "growth_tmp": 23.0, "optimum_tmp": 28.407, "optimum_ph": 7.016, "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": 0.0, "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", "glacialis" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }