{ "type": "genome", "identifier": "GCA_013697475.1", "organism": "Sphingomonas sp.", "title": "Sphingomonas sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "Monash University", "publication": [ {} ], "properties": { "assembly_accession": "GCA_013697475.1", "bioproject": "PRJNA630822", "biosample": "SAMN15052044", "wgs_master": "JACCWV000000000.1", "refseq_category": "na", "taxid": "28214", "species_taxid": "28214", "organism_name": "Sphingomonas sp.", "infraspecific_name": "", "isolate": "MGR_bin161", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/07/26", "asm_name": "ASM1369747v1", "submitter": "Monash University", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/697/475/GCA_013697475.1_ASM1369747v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-07-26", "dateModified": "2020-07-26", "datePublished": "2020-07-26", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas sp." ], "sample_taxid": [ "28214" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica: Mackay Glacier regions" ], "sample_host_location_id": [], "data_size": "0.363 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 41.67, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "1296081", "Number of Sequences": "360", "Longest Sequences (bp)": "12298", "N50 (bp)": "3640", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.3", "Number of CDSs": "1016", "Average Protein Length": "258.6", "Coding Ratio (%)": "60.8", "Number of rRNAs": "0", "Number of tRNAs": "38", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas sinipercae", "strain": "strain=HDW15C", "accession": "GCA_011302055.1", "taxid": 2714944, "species_taxid": 2714944, "relation_to_type": "type", "validated": true, "ani": 79.515, "matched_fragments": 166, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas sabuli", "strain": "strain=sand1-3", "accession": "GCA_014352855.1", "taxid": 2764186, "species_taxid": 2764186, "relation_to_type": "type", "validated": true, "ani": 79.3744, "matched_fragments": 152, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas mesophila", "strain": "strain=SYSUP0001", "accession": "GCA_003499275.1", "taxid": 2303576, "species_taxid": 2303576, "relation_to_type": "type", "validated": true, "ani": 79.205, "matched_fragments": 137, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas lutea", "strain": "strain=KCTC 23642", "accession": "GCA_014396785.1", "taxid": 1045317, "species_taxid": 1045317, "relation_to_type": "type", "validated": true, "ani": 79.0147, "matched_fragments": 134, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas lutea", "strain": "strain=KCTC 23642", "accession": "GCA_021497585.1", "taxid": 1045317, "species_taxid": 1045317, "relation_to_type": "type", "validated": true, "ani": 78.9867, "matched_fragments": 133, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas ginkgonis", "strain": "strain=HMF7854", "accession": "GCA_003970925.1", "taxid": 2315330, "species_taxid": 2315330, "relation_to_type": "type", "validated": true, "ani": 78.8344, "matched_fragments": 128, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas ginsengisoli An et al. 2013", "strain": "strain=KACC 16858", "accession": "GCA_009363895.1", "taxid": 363835, "species_taxid": 363835, "relation_to_type": "type", "validated": true, "ani": 78.4491, "matched_fragments": 131, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas segetis", "strain": "strain=YJ09", "accession": "GCA_009720245.1", "taxid": 1104779, "species_taxid": 1104779, "relation_to_type": "type", "validated": true, "ani": 78.4337, "matched_fragments": 131, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas kaistensis", "strain": "strain=DSM 16846", "accession": "GCA_011927725.1", "taxid": 298708, "species_taxid": 298708, "relation_to_type": "type", "validated": true, "ani": 78.1158, "matched_fragments": 131, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas rhizophila", "strain": "strain=KACC 19189", "accession": "GCA_014396585.1", "taxid": 2071607, "species_taxid": 2071607, "relation_to_type": "type", "validated": true, "ani": 78.0092, "matched_fragments": 128, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas jaspsi", "strain": "strain=DSM 18422", "accession": "GCA_000585415.1", "taxid": 392409, "species_taxid": 392409, "relation_to_type": "type", "validated": true, "ani": 77.7576, "matched_fragments": 113, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas piscis", "strain": "strain=HDW15B", "accession": "GCA_011300455.1", "taxid": 2714943, "species_taxid": 2714943, "relation_to_type": "type", "validated": true, "ani": 77.5902, "matched_fragments": 93, "total_fragments": 233, "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": 76.7028, "matched_fragments": 84, "total_fragments": 233, "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": 76.6801, "matched_fragments": 92, "total_fragments": 233, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 41.67, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_013812805.1", "gtdb_species": "s__Sphingomicrobium sp013812805", "ani": 81.6666, "matched_fragments": 180, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_013812825.1", "gtdb_species": "s__Sphingomicrobium sp013812825", "ani": 79.6795, "matched_fragments": 164, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_011302055.1", "gtdb_species": "s__Sphingomicrobium sinipercae", "ani": 79.515, "matched_fragments": 166, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_011053295.1", "gtdb_species": "s__Sphingomicrobium sp011053295", "ani": 79.4533, "matched_fragments": 120, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_014352855.1", "gtdb_species": "s__Sphingomicrobium sp014352855", "ani": 79.3744, "matched_fragments": 152, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_003499275.1", "gtdb_species": "s__Sphingomicrobium mesophila", "ani": 79.2737, "matched_fragments": 135, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_013817375.1", "gtdb_species": "s__Sphingomicrobium sp013817375", "ani": 79.1815, "matched_fragments": 146, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_014396785.1", "gtdb_species": "s__Sphingomicrobium lutea", "ani": 79.0147, "matched_fragments": 134, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_000620665.1", "gtdb_species": "s__Sphingomicrobium sp000620665", "ani": 78.5875, "matched_fragments": 150, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_009720245.1", "gtdb_species": "s__Sphingomicrobium sp009720245", "ani": 78.4945, "matched_fragments": 129, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_009363895.1", "gtdb_species": "s__Sphingomicrobium ginsengisoli", "ani": 78.4491, "matched_fragments": 131, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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": "GCA_013816785.1", "gtdb_species": "s__Sphingomicrobium sp013816785", "ani": 78.3427, "matched_fragments": 118, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_014873795.1", "gtdb_species": "s__Sphingomicrobium sp014873795", "ani": 78.0536, "matched_fragments": 122, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_902806285.1", "gtdb_species": "s__Sphingomicrobium sp902806285", "ani": 77.962, "matched_fragments": 126, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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_000585415.1", "gtdb_species": "s__Sphingomicrobium jaspsi", "ani": 77.788, "matched_fragments": 112, "total_fragments": 233, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium", "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": -0.288, "cell_length": 0.14, "doubling_h": null, "growth_tmp": 28.338, "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": 0.586, "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": 0.98, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.019 }, "_gtdb_taxon": [ "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Sphingomonadales", "f__Sphingomonadaceae", "g__Sphingomicrobium", "s__" ], "_genome_taxon": [ "Sphingomonas", "sp.", "d__Bacteria", "p__Pseudomonadota", "c__Alphaproteobacteria", "o__Sphingomonadales", "f__Sphingomonadaceae", "g__Sphingomicrobium", "s__", "Bacteria", "Pseudomonadota", "Alphaproteobacteria", "Sphingomonadales", "Sphingomonadaceae", "Sphingomicrobium", "s", "", "" ], "_meo": [ { "id": "MEO_0000007", "label": "soil" } ], "quality": 2, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f" }