{ "type": "genome", "identifier": "GCF_001418225.1", "organism": "Pannonibacter indicus", "title": "Pannonibacter indicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001418225.1", "bioproject": "PRJNA224116", "biosample": "SAMN03801379", "wgs_master": "LIPT00000000.1", "refseq_category": "reference genome", "taxid": "466044", "species_taxid": "466044", "organism_name": "Pannonibacter indicus", "infraspecific_name": "strain=DSM 23407", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/10/28", "asm_name": "ASM141822v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_001418225.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/418/225/GCF_001418225.1_ASM141822v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4170676", "genome_size_ungapped": "4170000", "gc_percent": "63.500000", "replicon_count": "0", "scaffold_count": "36", "contig_count": "36", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001418225.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "3886", "protein_coding_gene_count": "3769", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-10-28", "dateModified": "2015-10-28", "datePublished": "2015-10-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Pannonibacter indicus" ], "sample_taxid": [ "466044" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: Orissa, Athamallik" ], "sample_host_location_id": [], "data_size": "1.156 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)": "4170676", "Number of Sequences": "36", "Longest Sequences (bp)": "646376", "N50 (bp)": "216090", "Gap Ratio (%)": "0.016208", "GCcontent (%)": "63.5", "Number of CDSs": "3841", "Average Protein Length": "317.1", "Coding Ratio (%)": "87.6", "Number of rRNAs": "5", "Number of tRNAs": "56", "Number of CRISPRs": "4" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pannonibacter indicus", "strain": "strain=DSM 23407", "accession": "GCA_001517385.1", "taxid": 466044, "species_taxid": 466044, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1370, "total_fragments": 1373, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pannonibacter indicus", "strain": "strain=DSM 23407", "accession": "GCA_001418225.1", "taxid": 466044, "species_taxid": 466044, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1370, "total_fragments": 1373, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pannonibacter phragmitetus", "strain": "strain=NCTC13350", "accession": "GCA_900454465.1", "taxid": 121719, "species_taxid": 121719, "relation_to_type": "suspected-type", "validated": true, "ani": 93.6434, "matched_fragments": 1261, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter phragmitetus", "strain": "strain=DSM 14782", "accession": "GCA_000382365.1", "taxid": 121719, "species_taxid": 121719, "relation_to_type": "suspected-type", "validated": true, "ani": 93.5917, "matched_fragments": 1250, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pannonibacter carbonis", "strain": "strain=Q4.6", "accession": "GCA_003012935.1", "taxid": 2067569, "species_taxid": 2067569, "relation_to_type": "type", "validated": true, "ani": 80.9124, "matched_fragments": 759, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stappia albiluteola", "strain": "strain=F7233", "accession": "GCA_014050225.1", "taxid": 2758565, "species_taxid": 2758565, "relation_to_type": "type", "validated": true, "ani": 78.488, "matched_fragments": 437, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xanthobacter oligotrophicus", "strain": "strain=29k", "accession": "GCA_008364685.1", "taxid": 2607286, "species_taxid": 2607286, "relation_to_type": "type", "validated": true, "ani": 77.3256, "matched_fragments": 266, "total_fragments": 1373, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Starkeya novella", 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"d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter", "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_000192745.1", "gtdb_species": "s__Polymorphum gilvum", "ani": 79.9774, "matched_fragments": 622, "total_fragments": 1373, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum", "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_903970965.1", "gtdb_species": "s__Aureimonas sp903970965", "ani": 77.1161, "matched_fragments": 199, "total_fragments": 1373, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas", "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": -0.523, "cell_length": 0.301, "doubling_h": null, "growth_tmp": 28.0, "optimum_tmp": 33.0, "optimum_ph": null, "genome_size": 4170676.0, "gc_content": 63.432, "coding_genes": 5007.333, "rRNA16S_genes": 3.0, "tRNA_genes": 54.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 0.0, "thermophilic_range_tmp": 1.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pannonibacter", "indicus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }