{ "type": "genome", "identifier": "GCF_000832545.1", "organism": "Pedobacter lusitanus", "title": "Pedobacter lusitanus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "University of Aveiro", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000832545.1", "bioproject": "PRJNA224116", "biosample": "SAMN03291000", "wgs_master": "JXRA00000000.1", "refseq_category": "na", "taxid": "1503925", "species_taxid": "1503925", "organism_name": "Pedobacter lusitanus", "infraspecific_name": "strain=NL19", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2015/02/05", "asm_name": "ASM83254v1", "asm_submitter": "University of Aveiro", "gbrs_paired_asm": "GCA_000832545.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/832/545/GCF_000832545.1_ASM83254v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5988187", "genome_size_ungapped": "5988187", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "201", "contig_count": "201", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000832545.1-RS_2025_01_06", "annotation_date": "2025-01-06", "total_gene_count": "5386", "protein_coding_gene_count": "5224", "non_coding_gene_count": "65", "pubmed_id": "25814603" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2015-02-05", "dateModified": "2015-02-05", "datePublished": "2015-02-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter lusitanus" ], "sample_taxid": [ "1503925" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Portugal: Quinta do Bispo, Viseu" ], "sample_host_location_id": [], "data_size": "1.700 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)": "5988187", "Number of Sequences": "201", "Longest Sequences (bp)": "180540", "N50 (bp)": "57420", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.0", "Number of CDSs": "5200", "Average Protein Length": "336.0", "Coding Ratio (%)": "87.5", "Number of rRNAs": "5", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter lusitanus", "strain": "strain=NL19", "accession": "GCA_000832545.1", "taxid": 1503925, "species_taxid": 1503925, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1895, "total_fragments": 1908, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter cryoconitis", "strain": "strain=DSM 14825", "accession": "GCA_003259615.1", "taxid": 188932, "species_taxid": 188932, "relation_to_type": "suspected-type", "validated": true, "ani": 82.7682, "matched_fragments": 1106, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter hartonius", "strain": "strain=DSM 19033", "accession": "GCA_900107535.1", "taxid": 425514, "species_taxid": 425514, "relation_to_type": "type", "validated": true, "ani": 79.746, "matched_fragments": 456, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter westerhofensis", "strain": "strain=DSM 19036", "accession": "GCA_900182595.1", "taxid": 425512, "species_taxid": 425512, "relation_to_type": "type", "validated": true, "ani": 79.5297, "matched_fragments": 445, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter antarcticus", "strain": "strain=ATCC 51969", "accession": "GCA_900112985.1", "taxid": 34086, "species_taxid": 34086, "relation_to_type": "type", "validated": true, "ani": 79.1677, "matched_fragments": 357, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter antarcticus", "strain": "strain=4BY", "accession": "GCA_000722885.1", "taxid": 34086, "species_taxid": 34086, "relation_to_type": "type", "validated": true, "ani": 79.111, "matched_fragments": 351, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter metabolipauper", "strain": "strain=DSM 19035", "accession": "GCA_004362715.1", "taxid": 425513, "species_taxid": 425513, "relation_to_type": "type", "validated": true, "ani": 78.2373, "matched_fragments": 257, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter foliorum", "strain": "strain=LMG 31463", "accession": "GCA_013266735.1", "taxid": 2739058, "species_taxid": 2739058, "relation_to_type": "type", "validated": true, "ani": 78.1834, "matched_fragments": 257, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter steynii", "strain": "strain=DSM 19110", "accession": "GCA_900103665.1", "taxid": 430522, "species_taxid": 430522, "relation_to_type": "type", "validated": true, "ani": 78.1304, "matched_fragments": 360, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter nanyangensis", "strain": "strain=Q-4", "accession": "GCA_003313505.1", "taxid": 1562389, "species_taxid": 1562389, "relation_to_type": "type", "validated": true, "ani": 77.3069, "matched_fragments": 99, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter aquae", "strain": "strain=CJ43", "accession": "GCA_008195825.1", "taxid": 2605747, "species_taxid": 2605747, "relation_to_type": "type", "validated": true, "ani": 76.9525, "matched_fragments": 76, "total_fragments": 1908, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000832545.1", "gtdb_species": "s__Pedobacter lusitanus", "ani": 100.0, "matched_fragments": 1895, "total_fragments": 1908, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "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_014200605.1", "gtdb_species": "s__Pedobacter cryoconitis_B", "ani": 83.5552, "matched_fragments": 1212, "total_fragments": 1908, "gtdb_taxonomy": 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"gc_content": 42.651, "coding_genes": 4725.333, "rRNA16S_genes": 4.333, "tRNA_genes": 57.25, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.281, "range_salinity": null, "facultative_respiration": 0.031, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.968, "mesophilic_range_tmp": 0.5, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.5, "bacillus_cell_shape": 0.939, "coccus_cell_shape": 0.06, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "lusitanus" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }