{ "type": "genome", "identifier": "GCF_900564155.1", "organism": "Pedobacter schmidteae", "title": "Pedobacter schmidteae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "URMITE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900564155.1", "bioproject": "PRJNA224116", "biosample": "SAMEA4926131", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2201271", "species_taxid": "2201271", "organism_name": "Pedobacter schmidteae", "infraspecific_name": "strain=eg", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/09/25", "asm_name": "PRJEB26455", "asm_submitter": "URMITE", "gbrs_paired_asm": "GCA_900564155.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/564/155/GCF_900564155.1_PRJEB26455", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6198518", "genome_size_ungapped": "6198518", "gc_percent": "41.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900564155.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "5022", "protein_coding_gene_count": "4941", "non_coding_gene_count": "75", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-09-25", "dateModified": "2018-09-25", "datePublished": "2018-09-25", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter schmidteae" ], "sample_taxid": [ "2201271" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.750 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)": "6198518", "Number of Sequences": "1", "Longest Sequences (bp)": "6198518", "N50 (bp)": "6198518", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "41.1", "Number of CDSs": "4929", "Average Protein Length": "380.6", "Coding Ratio (%)": "90.8", "Number of rRNAs": "13", "Number of tRNAs": "58", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter schmidteae", "strain": "strain=eg", "accession": "GCA_900564155.1", "taxid": 2201271, "species_taxid": 2201271, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2065, "total_fragments": 2066, "ani_threshold": 95, "status": "conclusive" }, { "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": 80.1944, "matched_fragments": 795, "total_fragments": 2066, "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": 80.1155, "matched_fragments": 812, "total_fragments": 2066, "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": 80.0466, "matched_fragments": 697, "total_fragments": 2066, "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": 79.9865, "matched_fragments": 704, "total_fragments": 2066, "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": 79.6681, "matched_fragments": 739, "total_fragments": 2066, "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": 78.7349, "matched_fragments": 423, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter steynii", "strain": "strain=DSM 19110", "accession": "GCA_900103665.1", "taxid": 430522, "species_taxid": 430522, 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77.6041, "matched_fragments": 187, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrophilus", "strain": "strain=CCM 8644", "accession": "GCA_001652725.1", "taxid": 1826909, "species_taxid": 1826909, "relation_to_type": "type", "validated": true, "ani": 76.5714, "matched_fragments": 69, "total_fragments": 2066, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900564155.1", "gtdb_species": "s__Pedobacter sp900564155", "ani": 100.0, "matched_fragments": 2064, "total_fragments": 2066, "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_004331685.1", "gtdb_species": "s__Pedobacter sp004331685", "ani": 80.1953, "matched_fragments": 793, "total_fragments": 2066, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.88", "min_intra_species_ani": "97.88", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900100435.1", "gtdb_species": "s__Pedobacter sp900100435", "ani": 80.1723, "matched_fragments": 829, "total_fragments": 2066, "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": "-" }, { "accession": "GCF_900176505.1", "gtdb_species": "s__Pedobacter nyackensis", "ani": 80.1277, "matched_fragments": 810, "total_fragments": 2066, "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_000023825.1", "gtdb_species": "s__Pedobacter heparinus", "ani": 80.0528, "matched_fragments": 697, "total_fragments": 2066, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.29", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900176535.1", 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "schmidteae" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }