{ "type": "genome", "identifier": "GCF_900182875.1", "organism": "Novosphingobium panipatense", "title": "Novosphingobium panipatense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900182875.1", "bioproject": "PRJNA224116", "biosample": "SAMN06296065", "wgs_master": "FXUI00000000.1", "refseq_category": "reference genome", "taxid": "428991", "species_taxid": "428991", "organism_name": "Novosphingobium panipatense", "infraspecific_name": "strain=SM16", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2023/04/08", "asm_name": "IMG-taxon 2706794921 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900182875.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/182/875/GCF_900182875.1_IMG-taxon_2706794921_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4079279", "genome_size_ungapped": "4079269", "gc_percent": "64.000000", "replicon_count": "0", "scaffold_count": "63", "contig_count": "63", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900182875.1-RS_2024_05_22", "annotation_date": "2024-05-22", "total_gene_count": "3961", "protein_coding_gene_count": "3824", "non_coding_gene_count": "62", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2023-04-08", "dateModified": "2023-04-08", "datePublished": "2023-04-08", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium panipatense" ], "sample_taxid": [ "428991" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.140 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)": "4079279", "Number of Sequences": "63", "Longest Sequences (bp)": "620391", "N50 (bp)": "294556", "Gap Ratio (%)": "0.000245", "GCcontent (%)": "64.2", "Number of CDSs": "3898", "Average Protein Length": "312.3", "Coding Ratio (%)": "89.5", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium guangzhouense", "strain": "strain=SA925", "accession": "GCA_002896965.1", 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"relation_to_type": "type", "validated": true, "ani": 80.5692, "matched_fragments": 490, "total_fragments": 1326, "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": 80.3698, "matched_fragments": 513, "total_fragments": 1326, "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": 80.3669, "matched_fragments": 519, "total_fragments": 1326, "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": 80.2759, "matched_fragments": 548, "total_fragments": 1326, "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": 79.9538, "matched_fragments": 370, "total_fragments": 1326, "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": 79.7701, "matched_fragments": 478, "total_fragments": 1326, "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": 79.7359, "matched_fragments": 485, "total_fragments": 1326, "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": 79.685, "matched_fragments": 467, "total_fragments": 1326, "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": 79.5911, "matched_fragments": 547, "total_fragments": 1326, "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": 79.4872, "matched_fragments": 480, "total_fragments": 1326, "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": 79.3492, "matched_fragments": 475, "total_fragments": 1326, "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": 78.883, "matched_fragments": 365, "total_fragments": 1326, "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": 78.7947, "matched_fragments": 369, "total_fragments": 1326, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002916655.1", "gtdb_species": "s__Novosphingobium sp002916655", "ani": 98.351, "matched_fragments": 1023, "total_fragments": 1326, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "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_002896965.1", "gtdb_species": "s__Novosphingobium guangzhouense", "ani": 82.0014, "matched_fragments": 715, "total_fragments": 1326, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", 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