{ "type": "genome", "identifier": "GCF_004362715.1", "organism": "Pedobacter metabolipauper", "title": "Pedobacter metabolipauper", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004362715.1", "bioproject": "PRJNA224116", "biosample": "SAMN04489865", "wgs_master": "SNYC00000000.1", "refseq_category": "reference genome", "taxid": "425513", "species_taxid": "425513", "organism_name": "Pedobacter metabolipauper", "infraspecific_name": "strain=DSM 19035", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/22", "asm_name": "ASM436271v1", "asm_submitter": "DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_004362715.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/362/715/GCF_004362715.1_ASM436271v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5251143", "genome_size_ungapped": "5250421", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "11", "contig_count": "11", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004362715.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4565", "protein_coding_gene_count": "4505", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-22", "dateModified": "2019-03-22", "datePublished": "2019-03-22", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter metabolipauper" ], "sample_taxid": [ "425513" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.485 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)": "5251143", "Number of Sequences": "11", "Longest Sequences (bp)": "1474365", "N50 (bp)": "1349253", "Gap Ratio (%)": "0.013749", "GCcontent (%)": "40.6", "Number of CDSs": "4492", "Average Protein Length": "352.2", "Coding Ratio (%)": "90.4", "Number of rRNAs": "5", "Number of tRNAs": "41", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter metabolipauper", "strain": "strain=DSM 19035", "accession": "GCA_004362715.1", "taxid": 425513, "species_taxid": 425513, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1743, "total_fragments": 1744, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter foliorum", "strain": "strain=LMG 31463", "accession": "GCA_013266735.1", "taxid": 2739058, "species_taxid": 2739058, "relation_to_type": "type", "validated": true, "ani": 78.9868, "matched_fragments": 419, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter hiemivivus", "strain": "strain=RP-3-8", "accession": "GCA_004331685.1", "taxid": 2530454, "species_taxid": 2530454, "relation_to_type": "type", "validated": true, "ani": 78.9575, "matched_fragments": 348, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter panaciterrae", "strain": "strain=LMG 23400", "accession": "GCA_013204795.1", "taxid": 363849, "species_taxid": 363849, "relation_to_type": "type", "validated": true, "ani": 78.912, "matched_fragments": 441, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychroterrae", "strain": "strain=RP-1-14", "accession": "GCA_004331695.1", "taxid": 2530453, "species_taxid": 2530453, "relation_to_type": "type", "validated": true, "ani": 78.8634, "matched_fragments": 366, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter frigoris", "strain": "strain=RP-3-15", "accession": "GCA_005116445.1", "taxid": 2571272, "species_taxid": 2571272, "relation_to_type": "type", "validated": true, "ani": 78.858, "matched_fragments": 407, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter nyackensis", "strain": "strain=DSM 19625", "accession": "GCA_900176505.1", "taxid": 475255, "species_taxid": 475255, "relation_to_type": "type", "validated": true, "ani": 78.6747, "matched_fragments": 370, "total_fragments": 1744, "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": 78.6641, "matched_fragments": 414, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter heparinus", "strain": "strain=DSM 2366", "accession": "GCA_000410815.1", "taxid": 984, "species_taxid": 984, "relation_to_type": "type", "validated": true, "ani": 78.6401, "matched_fragments": 364, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter schmidteae", "strain": "strain=eg", "accession": "GCA_900564155.1", "taxid": 2201271, "species_taxid": 2201271, "relation_to_type": "type", "validated": true, "ani": 78.6255, "matched_fragments": 344, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter heparinus", "strain": "strain=DSM 2366", "accession": "GCA_000023825.1", "taxid": 984, "species_taxid": 984, "relation_to_type": "type", "validated": true, "ani": 78.6211, "matched_fragments": 363, "total_fragments": 1744, "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": 78.6153, "matched_fragments": 271, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter caeni", "strain": "strain=DSM 16990", "accession": "GCA_900129215.1", "taxid": 288992, "species_taxid": 288992, "relation_to_type": "type", "validated": true, "ani": 78.5878, "matched_fragments": 407, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter africanus", "strain": "strain=DSM 12126", "accession": "GCA_900176535.1", "taxid": 151894, "species_taxid": 151894, "relation_to_type": "type", "validated": true, "ani": 78.481, "matched_fragments": 343, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter mucosus", "strain": "strain=Q8-18", "accession": "GCA_022200785.1", "taxid": 2895286, "species_taxid": 2895286, "relation_to_type": "type", "validated": true, "ani": 77.9662, "matched_fragments": 121, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter polaris", "strain": "strain=RP-3-22", "accession": "GCA_005116505.1", "taxid": 2571273, "species_taxid": 2571273, "relation_to_type": "type", "validated": true, "ani": 77.9575, "matched_fragments": 178, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter ginsenosidivorax", "strain": "strain=KHI28", "accession": "GCA_007971525.1", "taxid": 862126, "species_taxid": 862126, "relation_to_type": "type", "validated": true, "ani": 76.5576, "matched_fragments": 71, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter conchicola", "strain": "strain=MYSH2", "accession": "GCA_003432115.1", "taxid": 2303333, "species_taxid": 2303333, "relation_to_type": "type", "validated": true, "ani": 76.0582, "matched_fragments": 69, "total_fragments": 1744, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004362715.1", "gtdb_species": "s__Pedobacter metabolipauper", "ani": 100.0, "matched_fragments": 1743, "total_fragments": 1744, "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" }, { 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