{ "type": "genome", "identifier": "GCF_021227995.1", "organism": "Novosphingobium kaempferiae", "title": "Novosphingobium kaempferiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Faculty of Science, Chulalongkorn University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_021227995.1", "bioproject": "PRJNA224116", "biosample": "SAMN23259152", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2896849", "species_taxid": "2896849", "organism_name": "Novosphingobium kaempferiae", "infraspecific_name": "strain=Sx8-5", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/12/18", "asm_name": "ASM2122799v1", "asm_submitter": "Faculty of Science, Chulalongkorn University", "gbrs_paired_asm": "GCA_021227995.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/021/227/995/GCF_021227995.1_ASM2122799v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5698134", "genome_size_ungapped": "5698134", "gc_percent": "66.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_021227995.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "5218", "protein_coding_gene_count": "5120", "non_coding_gene_count": "58", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-12-18", "dateModified": "2021-12-18", "datePublished": "2021-12-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium kaempferiae" ], "sample_taxid": [ "2896849" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Thailand: Bangkok" ], "sample_host_location_id": [], "data_size": "1.562 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)": "5698134", "Number of Sequences": "1", "Longest Sequences (bp)": "5698134", "N50 (bp)": "5698134", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.0", "Number of CDSs": "5138", "Average Protein Length": "329.5", "Coding Ratio (%)": "89.1", "Number of rRNAs": "3", "Number of tRNAs": "57", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium guangzhouense", "strain": "strain=SA925", "accession": "GCA_002896965.1", "taxid": 1850347, "species_taxid": 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"validated": true, "ani": 82.0479, "matched_fragments": 672, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium lindaniclasticum", "strain": "strain=LE124", "accession": "GCA_000445125.1", "taxid": 1329895, "species_taxid": 1329895, "relation_to_type": "type", "validated": true, "ani": 82.0129, "matched_fragments": 768, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium pentaromativorans", "strain": "strain=US6-1", "accession": "GCA_000767465.1", "taxid": 205844, "species_taxid": 205844, "relation_to_type": "type", "validated": true, "ani": 81.4407, "matched_fragments": 621, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium pentaromativorans", "strain": "strain=US6-1", "accession": "GCA_000235975.2", "taxid": 205844, "species_taxid": 205844, "relation_to_type": "type", "validated": true, "ani": 81.4289, "matched_fragments": 605, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium aureum", "strain": "strain=YJ-S2-02", "accession": "GCA_015865035.1", "taxid": 2792964, "species_taxid": 2792964, "relation_to_type": "type", "validated": true, "ani": 81.3662, "matched_fragments": 728, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium mathurense", "strain": "strain=SM117", "accession": "GCA_900168325.1", "taxid": 428990, "species_taxid": 428990, "relation_to_type": "type", "validated": true, "ani": 81.3123, "matched_fragments": 669, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium endophyticum", "strain": "strain=CGMCC 1.15095", "accession": "GCA_014640675.1", "taxid": 1955250, "species_taxid": 1955250, "relation_to_type": "type", "validated": true, "ani": 81.2135, "matched_fragments": 635, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium indicum", "strain": "strain=CGMCC 1.6784", "accession": "GCA_014645195.1", "taxid": 462949, "species_taxid": 462949, "relation_to_type": "type", "validated": true, "ani": 81.1608, "matched_fragments": 745, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium decolorationis", "strain": "strain=502str22", "accession": "GCA_018417475.1", "taxid": 2698673, "species_taxid": 2698673, "relation_to_type": "type", "validated": true, "ani": 80.8639, "matched_fragments": 681, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium profundi", "strain": "strain=F72", "accession": "GCA_018491765.1", "taxid": 1774954, "species_taxid": 1774954, "relation_to_type": "type", "validated": true, "ani": 80.8249, "matched_fragments": 740, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium colocasiae", "strain": "strain=KCTC 32255", "accession": "GCA_014652555.1", "taxid": 1256513, "species_taxid": 1256513, "relation_to_type": "type", "validated": true, "ani": 80.7348, "matched_fragments": 605, "total_fragments": 1899, "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": 79.849, "matched_fragments": 563, "total_fragments": 1899, "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": 79.6466, "matched_fragments": 566, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium aquimarinum", "strain": "strain=M24A2M", "accession": "GCA_009746585.1", "taxid": 2682494, "species_taxid": 2682494, "relation_to_type": "type", "validated": true, "ani": 79.6203, "matched_fragments": 537, "total_fragments": 1899, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001742225.1", "gtdb_species": "s__Novosphingobium resinovorum", "ani": 86.4614, "matched_fragments": 1182, "total_fragments": 1899, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.22", "min_intra_species_ani": "97.83", "mean_intra_species_af": "0.80", "min_intra_species_af": "0.78", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_002896965.1", "gtdb_species": "s__Novosphingobium 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