{ "type": "genome", "identifier": "GCF_000708285.2", "organism": "Pedobacter borealis DSM 19626", "title": "Pedobacter borealis DSM 19626", "description": "na", "data type": "Genome sequencing and assembly", "organization": "GCAT-SEEK", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000708285.2", "bioproject": "PRJNA224116", "biosample": "SAMN02597035", "wgs_master": "JAUG00000000.1", "refseq_category": "reference genome", "taxid": "1454007", "species_taxid": "475254", "organism_name": "Pedobacter borealis DSM 19626", "infraspecific_name": "strain=DSM 19626", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Minor", "genome_rep": "Full", "seq_rel_date": "2014/06/16", "asm_name": "Genome Assembly for Pedobacter borealis DSM19626", "asm_submitter": "GCAT-SEEK", "gbrs_paired_asm": "GCA_000708285.2", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/708/285/GCF_000708285.2_Genome_Assembly_for_Pedobacter_borealis_DSM19626", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5544917", "genome_size_ungapped": "5544917", "gc_percent": "38.500000", "replicon_count": "0", "scaffold_count": "216", "contig_count": "216", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000708285.2-RS_2024_04_29", "annotation_date": "2024-04-29", "total_gene_count": "4716", "protein_coding_gene_count": "4626", "non_coding_gene_count": "56", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-06-16", "dateModified": "2014-06-16", "datePublished": "2014-06-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter borealis DSM 19626" ], "sample_taxid": [ "1454007" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Western Montana" ], "sample_host_location_id": [], "data_size": "1.573 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)": "5544917", "Number of Sequences": "216", "Longest Sequences (bp)": "202646", "N50 (bp)": "47779", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "38.4", "Number of CDSs": "4546", "Average Protein Length": "334.4", "Coding Ratio (%)": "82.3", "Number of rRNAs": "3", "Number of tRNAs": "52", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter borealis", "strain": "strain=DSM 19626", "accession": "GCA_000708285.2", "taxid": 475254, "species_taxid": 475254, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1735, "total_fragments": 1746, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter kyonggii", "strain": "strain=K-4-11-1", "accession": "GCA_004310665.1", "taxid": 1926871, "species_taxid": 1926871, "relation_to_type": "type", "validated": true, "ani": 92.1421, "matched_fragments": 1234, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ginsenosidimutans", "strain": "strain=KACC 14530", "accession": "GCA_001442625.1", "taxid": 687842, "species_taxid": 687842, "relation_to_type": "type", "validated": true, "ani": 92.0855, "matched_fragments": 1244, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter psychrodurus", "strain": "strain=RP-3-21", "accession": "GCA_004331735.1", "taxid": 2530456, "species_taxid": 2530456, "relation_to_type": "type", 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1059, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter miscanthi", "strain": "strain=RS10", "accession": "GCA_003315595.1", "taxid": 2259170, "species_taxid": 2259170, "relation_to_type": "type", "validated": true, "ani": 83.1586, "matched_fragments": 1005, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter ghigonis", "strain": "strain=Marseille-Q2390", "accession": "GCA_903166585.1", "taxid": 2730403, "species_taxid": 2730403, "relation_to_type": "type", "validated": true, "ani": 81.9769, "matched_fragments": 959, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter agri", "strain": "strain=R11", "accession": "GCA_009928685.1", "taxid": 2695265, "species_taxid": 2695265, "relation_to_type": "type", "validated": true, "ani": 76.9702, "matched_fragments": 94, "total_fragments": 1746, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000708285.2", "gtdb_species": "s__Pedobacter borealis", "ani": 100.0, "matched_fragments": 1735, "total_fragments": 1746, "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_018613605.1", "gtdb_species": "s__Pedobacter sp018613605", "ani": 93.7393, "matched_fragments": 1224, "total_fragments": 1746, "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", 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_003387415.1", "gtdb_species": "s__Pedobacter sp003387415", "ani": 91.197, "matched_fragments": 1194, "total_fragments": 1746, "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_003054145.1", "gtdb_species": "s__Pedobacter sp003054145", "ani": 89.5976, "matched_fragments": 1250, "total_fragments": 1746, "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", 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