{ "type": "genome", "identifier": "GCF_000802225.1", "organism": "Novosphingobium malaysiense", "title": "Novosphingobium malaysiense", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Malaya", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000802225.1", "bioproject": "PRJNA224116", "biosample": "SAMN03070119", "wgs_master": "JTDI00000000.1", "refseq_category": "reference genome", "taxid": "1348853", "species_taxid": "1348853", "organism_name": "Novosphingobium malaysiense", "infraspecific_name": "strain=MUSC 273", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/12/16", "asm_name": "ASM80222v1", "asm_submitter": "University of Malaya", "gbrs_paired_asm": "GCA_000802225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/802/225/GCF_000802225.1_ASM80222v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5027021", "genome_size_ungapped": "5027021", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "85", "contig_count": "85", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000802225.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "4796", "protein_coding_gene_count": "4685", "non_coding_gene_count": "55", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-12-16", "dateModified": "2014-12-16", "datePublished": "2014-12-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Novosphingobium malaysiense" ], "sample_taxid": [ "1348853" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Malaysia" ], "sample_host_location_id": [], "data_size": "1.402 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 28.0, "max": 28.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5027021", "Number of Sequences": "85", "Longest Sequences (bp)": "1344633", "N50 (bp)": "631941", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "63.4", "Number of CDSs": "4675", "Average Protein Length": "321.3", "Coding Ratio (%)": "89.6", "Number of rRNAs": "3", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Novosphingobium malaysiense", "strain": "strain=MUSC 273", "accession": "GCA_000802225.1", "taxid": 1348853, "species_taxid": 1348853, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1659, "total_fragments": 1659, "ani_threshold": 95, "status": "conclusive" }, { "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": 86.5411, "matched_fragments": 1034, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium naphthalenivorans", "strain": "strain=NBRC 102051", "accession": "GCA_001590985.1", "taxid": 273168, "species_taxid": 273168, "relation_to_type": "type", "validated": true, "ani": 83.1125, "matched_fragments": 783, "total_fragments": 1659, "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": 81.7771, "matched_fragments": 676, "total_fragments": 1659, "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": 81.7018, "matched_fragments": 656, "total_fragments": 1659, "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": 81.2903, "matched_fragments": 660, "total_fragments": 1659, "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": 80.9149, "matched_fragments": 679, "total_fragments": 1659, "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": 80.6212, "matched_fragments": 647, "total_fragments": 1659, "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": 80.524, "matched_fragments": 601, "total_fragments": 1659, "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": 80.296, "matched_fragments": 611, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Novosphingobium silvae", "strain": "strain=FGD1", "accession": "GCA_009856825.1", "taxid": 2692619, "species_taxid": 2692619, "relation_to_type": "type", "validated": true, "ani": 80.1474, "matched_fragments": 584, "total_fragments": 1659, "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": 79.6516, "matched_fragments": 523, "total_fragments": 1659, "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": 79.4083, "matched_fragments": 453, "total_fragments": 1659, "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": 79.2918, "matched_fragments": 448, "total_fragments": 1659, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000802225.1", "gtdb_species": "s__Novosphingobium malaysiense", "ani": 100.0, "matched_fragments": 1659, "total_fragments": 1659, "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_014645195.1", "gtdb_species": "s__Novosphingobium indicum", "ani": 86.5319, "matched_fragments": 1035, "total_fragments": 1659, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.92", "min_intra_species_ani": "97.92", "mean_intra_species_af": "0.77", "min_intra_species_af": "0.77", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001590985.1", "gtdb_species": "s__Novosphingobium naphthalenivorans", "ani": 83.1043, "matched_fragments": 784, "total_fragments": 1659, "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": "-" }, { "accession": "GCF_000767465.1", "gtdb_species": "s__Novosphingobium pentaromativorans", "ani": 81.7771, "matched_fragments": 676, "total_fragments": 1659, 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Novosphingobium", "malaysiense" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }