{ "type": "genome", "identifier": "GCF_011300455.1", "organism": "Sphingomonas piscis", "title": "Sphingomonas piscis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kyung Hee University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_011300455.1", "bioproject": "PRJNA224116", "biosample": "SAMN14260682", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2714943", "species_taxid": "2714943", "organism_name": "Sphingomonas piscis", "infraspecific_name": "strain=HDW15B", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/03/16", "asm_name": "ASM1130045v1", "asm_submitter": "Kyung Hee University", "gbrs_paired_asm": "GCA_011300455.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/011/300/455/GCF_011300455.1_ASM1130045v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "2718035", "genome_size_ungapped": "2718035", "gc_percent": "63.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_011300455.1-RS_2024_05_05", "annotation_date": "2024-05-05", "total_gene_count": "2783", "protein_coding_gene_count": "2653", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-03-16", "dateModified": "2020-03-16", "datePublished": "2020-03-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas piscis" ], "sample_taxid": [ "2714943" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea" ], "sample_host_location_id": [], "data_size": "0.758 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)": "2718035", "Number of Sequences": "1", "Longest Sequences (bp)": "2718035", "N50 (bp)": "2718035", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.3", "Number of CDSs": "2816", "Average Protein Length": "291.9", "Coding Ratio (%)": "90.7", "Number of rRNAs": "3", "Number of tRNAs": "50", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas piscis", "strain": "strain=HDW15B", "accession": "GCA_011300455.1", "taxid": 2714943, "species_taxid": 2714943, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 906, "total_fragments": 906, "ani_threshold": 95, "status": "conclusive" }, { "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": 79.1995, "matched_fragments": 317, "total_fragments": 906, "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": 79.1689, "matched_fragments": 344, "total_fragments": 906, "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": 79.0832, "matched_fragments": 301, "total_fragments": 906, "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": 79.081, "matched_fragments": 307, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas sinipercae", "strain": "strain=HDW15C", "accession": "GCA_011302055.1", "taxid": 2714944, "species_taxid": 2714944, "relation_to_type": "type", "validated": true, "ani": 79.0673, "matched_fragments": 318, "total_fragments": 906, "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": 79.0516, "matched_fragments": 311, "total_fragments": 906, "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": 78.9903, "matched_fragments": 328, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas arenae", "strain": "strain=SYSU D00720", "accession": "GCA_016924655.1", "taxid": 2812555, "species_taxid": 2812555, "relation_to_type": "type", "validated": true, "ani": 78.9901, "matched_fragments": 290, "total_fragments": 906, "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": 78.88, "matched_fragments": 303, "total_fragments": 906, "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": 78.8612, "matched_fragments": 284, "total_fragments": 906, "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": 78.7978, "matched_fragments": 274, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas spermidinifaciens", "strain": "strain=9NM-10", "accession": "GCA_002351485.1", "taxid": 1141889, "species_taxid": 1141889, "relation_to_type": "type", "validated": true, "ani": 77.7541, "matched_fragments": 208, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium fuliginis", "strain": "strain=DSM 18781", "accession": "GCA_004152845.1", "taxid": 336203, "species_taxid": 336203, "relation_to_type": "type", "validated": true, "ani": 77.6128, "matched_fragments": 192, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingobium fuliginis", "strain": "strain=CCM 7327", "accession": "GCA_014636045.1", "taxid": 336203, "species_taxid": 336203, "relation_to_type": "type", "validated": true, "ani": 77.6068, "matched_fragments": 189, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas corticis", "strain": "strain=36D10-4-7", "accession": "GCA_012035195.1", "taxid": 2722791, "species_taxid": 2722791, "relation_to_type": "type", "validated": true, "ani": 77.6032, "matched_fragments": 211, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Neorhizobium lilium", "strain": "strain=24NR", "accession": "GCA_004053875.1", "taxid": 2503024, "species_taxid": 2503024, "relation_to_type": "type", "validated": true, "ani": 75.8956, "matched_fragments": 52, "total_fragments": 906, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_011300455.1", "gtdb_species": "s__Sphingomicrobium piscis", "ani": 100.0, "matched_fragments": 906, "total_fragments": 906, "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": "conclusive" }, { "accession": "GCF_009363895.1", "gtdb_species": "s__Sphingomicrobium ginsengisoli", "ani": 79.2145, "matched_fragments": 316, "total_fragments": 906, "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": "GCF_003970925.1", "gtdb_species": "s__Sphingomicrobium sp003970925", "ani": 79.1689, "matched_fragments": 344, "total_fragments": 906, "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": 79.0989, "matched_fragments": 300, "total_fragments": 906, "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": 79.082, "matched_fragments": 317, "total_fragments": 906, "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": 79.0663, "matched_fragments": 310, "total_fragments": 906, "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_016924655.1", "gtdb_species": "s__Sphingomicrobium sp016924655", "ani": 78.9901, "matched_fragments": 290, "total_fragments": 906, "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": "GCF_014873475.1", "gtdb_species": "s__Sphingomicrobium sp014873475", "ani": 78.9452, "matched_fragments": 325, "total_fragments": 906, "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_014873375.1", "gtdb_species": "s__Sphingomicrobium sp014873375", "ani": 78.9418, "matched_fragments": 281, "total_fragments": 906, "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": "GCF_000585415.1", "gtdb_species": "s__Sphingomicrobium jaspsi", "ani": 78.9082, "matched_fragments": 300, "total_fragments": 906, "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_014396585.1", "gtdb_species": "s__Sphingomicrobium rhizophilum", "ani": 78.8254, "matched_fragments": 287, "total_fragments": 906, "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": 78.7978, "matched_fragments": 274, "total_fragments": 906, "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": 78.7676, "matched_fragments": 315, "total_fragments": 906, "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": 78.5765, "matched_fragments": 281, "total_fragments": 906, "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_902806265.1", "gtdb_species": "s__Sphingomicrobium sp902806265", "ani": 78.5412, "matched_fragments": 276, "total_fragments": 906, "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_003097155.1", "gtdb_species": "s__Sphingomicrobium sp003097155", "ani": 78.5224, "matched_fragments": 328, "total_fragments": 906, "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_013812805.1", "gtdb_species": "s__Sphingomicrobium sp013812805", "ani": 78.4193, "matched_fragments": 220, "total_fragments": 906, "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_001591045.1", "gtdb_species": "s__Sphingopyxis granuli", "ani": 77.9065, "matched_fragments": 182, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.56", "min_intra_species_ani": "96.77", "mean_intra_species_af": "0.81", "min_intra_species_af": "0.78", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_002351485.1", "gtdb_species": "s__Sphingomonas spermidinifaciens", "ani": 77.7562, "matched_fragments": 208, "total_fragments": 906, "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_001563265.1", "gtdb_species": "s__Sphingobium sp001563265", "ani": 77.4653, "matched_fragments": 188, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "97.84", "mean_intra_species_af": "0.74", "min_intra_species_af": "0.68", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001556185.1", "gtdb_species": "s__Sphingomonas sp001556185", "ani": 77.4388, "matched_fragments": 173, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.51", "min_intra_species_ani": "96.51", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014207235.1", "gtdb_species": "s__Sphingopyxis sp014207235", "ani": 77.3426, "matched_fragments": 185, "total_fragments": 906, "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_001562255.1", "gtdb_species": "s__Bosea sp001562255", "ani": 76.331, "matched_fragments": 84, "total_fragments": 906, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea", "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 }, "_genome_taxon": [ "Sphingomonas", "piscis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }