{ "type": "genome", "identifier": "GCF_900215335.1", "organism": "Pedobacter xixiisoli", "title": "Pedobacter xixiisoli", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900215335.1", "bioproject": "PRJNA224116", "biosample": "SAMN06297358", "wgs_master": "OCMT00000000.1", "refseq_category": "reference genome", "taxid": "1476464", "species_taxid": "1476464", "organism_name": "Pedobacter xixiisoli", "infraspecific_name": "strain=CGMCC 1.12803", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/09/28", "asm_name": "IMG-taxon 2721755864 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900215335.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/215/335/GCF_900215335.1_IMG-taxon_2721755864_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": "4974702", "genome_size_ungapped": "4974641", "gc_percent": "37.500000", "replicon_count": "0", "scaffold_count": "8", "contig_count": "8", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900215335.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4174", "protein_coding_gene_count": "4114", "non_coding_gene_count": "51", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-09-28", "dateModified": "2017-09-28", "datePublished": "2017-09-28", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter xixiisoli" ], "sample_taxid": [ "1476464" ], "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": "1.402 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)": "4974702", "Number of Sequences": "8", "Longest Sequences (bp)": "1521958", "N50 (bp)": "1401440", "Gap Ratio (%)": "0.001226", "GCcontent (%)": "37.7", "Number of CDSs": "4103", "Average Protein Length": "352.9", "Coding Ratio (%)": "87.3", "Number of rRNAs": "3", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter xixiisoli", "strain": "strain=CGMCC 1.12803", "accession": "GCA_900215335.1", "taxid": 1476464, 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81.5981, "matched_fragments": 871, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter chitinilyticus", "strain": "strain=CM134L-2", "accession": "GCA_003313385.1", "taxid": 2233776, "species_taxid": 2233776, "relation_to_type": "type", "validated": true, "ani": 80.036, "matched_fragments": 729, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter chitinilyticus", "strain": "strain=CM134L-2", "accession": "GCA_004025525.1", "taxid": 2233776, "species_taxid": 2233776, "relation_to_type": "type", "validated": true, "ani": 80.0217, "matched_fragments": 731, "total_fragments": 1654, "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": 79.4644, "matched_fragments": 591, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter frigiditerrae", "strain": "strain=RP-1-13", "accession": "GCA_004331645.1", "taxid": 2530452, "species_taxid": 2530452, "relation_to_type": "type", "validated": true, "ani": 77.9404, "matched_fragments": 363, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter kyungheensis", "strain": "strain=KACC 16221", "accession": "GCA_000812965.1", "taxid": 1069985, "species_taxid": 1069985, "relation_to_type": "type", "validated": true, "ani": 77.7773, "matched_fragments": 221, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter terrae", "strain": "strain=DSM 17933", "accession": "GCA_900100705.1", "taxid": 405671, "species_taxid": 405671, "relation_to_type": "type", "validated": true, "ani": 77.566, "matched_fragments": 220, "total_fragments": 1654, "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": 76.6477, "matched_fragments": 119, "total_fragments": 1654, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900215335.1", "gtdb_species": "s__Pedobacter xixiisoli", "ani": 100.0, "matched_fragments": 1654, "total_fragments": 1654, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_005925325.1", "gtdb_species": "s__Pedobacter 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610, "total_fragments": 1654, "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": "-" }, { "accession": "GCF_003313385.1", "gtdb_species": "s__Pedobacter chitinilyticus", "ani": 80.0395, "matched_fragments": 729, "total_fragments": 1654, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "95.89", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003313335.1", "gtdb_species": "s__Pedobacter zeaxanthinifaciens", "ani": 79.8184, "matched_fragments": 576, "total_fragments": 1654, 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