{ "type": "genome", "identifier": "GCF_005116445.1", "organism": "Pedobacter frigoris", "title": "Pedobacter frigoris", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Kyonggi University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_005116445.1", "bioproject": "PRJNA224116", "biosample": "SAMN11478357", "wgs_master": "SWBQ00000000.1", "refseq_category": "reference genome", "taxid": "2571272", "species_taxid": "2571272", "organism_name": "Pedobacter frigoris", "infraspecific_name": "strain=RP-3-15", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/05/02", "asm_name": "ASM511644v1", "asm_submitter": "Kyonggi University", "gbrs_paired_asm": "GCA_005116445.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/005/116/445/GCF_005116445.1_ASM511644v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4686568", "genome_size_ungapped": "4686568", "gc_percent": "40.000000", "replicon_count": "0", "scaffold_count": "20", "contig_count": "20", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_005116445.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4140", "protein_coding_gene_count": "4069", "non_coding_gene_count": "54", "pubmed_id": "32160145" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-05-02", "dateModified": "2019-05-02", "datePublished": "2019-05-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter frigoris" ], "sample_taxid": [ "2571272" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Canada: Cambridge Bay, NU" ], "sample_host_location_id": [], "data_size": "1.331 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)": "4686568", "Number of Sequences": "20", "Longest Sequences (bp)": "1477733", "N50 (bp)": "943723", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "40.1", "Number of CDSs": "3999", "Average Protein Length": "351.1", "Coding Ratio (%)": "89.9", "Number of rRNAs": "6", "Number of tRNAs": "43", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "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": 100.0, "matched_fragments": 1548, "total_fragments": 1551, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter panaciterrae", "strain": "strain=LMG 23400", "accession": "GCA_013204795.1", "taxid": 363849, "species_taxid": 363849, "relation_to_type": "type", "validated": true, "ani": 79.6642, "matched_fragments": 447, "total_fragments": 1551, "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": 79.5161, "matched_fragments": 457, "total_fragments": 1551, "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": 79.3875, "matched_fragments": 388, "total_fragments": 1551, "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": 79.0264, "matched_fragments": 400, "total_fragments": 1551, "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": 78.9917, "matched_fragments": 415, "total_fragments": 1551, "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": 78.9798, "matched_fragments": 376, "total_fragments": 1551, "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": 78.9527, "matched_fragments": 404, "total_fragments": 1551, "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": 78.8916, "matched_fragments": 382, "total_fragments": 1551, "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": 78.8431, "matched_fragments": 380, "total_fragments": 1551, "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": 78.7986, "matched_fragments": 399, "total_fragments": 1551, "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": 78.7744, "matched_fragments": 412, "total_fragments": 1551, "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": 78.5455, "matched_fragments": 237, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter duraquae", "strain": "strain=DSM 19034", "accession": "GCA_004362245.1", "taxid": 425511, "species_taxid": 425511, "relation_to_type": "type", "validated": true, "ani": 78.2788, "matched_fragments": 222, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "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": 78.2511, "matched_fragments": 237, "total_fragments": 1551, "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": 77.3385, "matched_fragments": 173, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter segetis", "strain": "strain=SD-g", "accession": "GCA_016522075.1", "taxid": 2793071, "species_taxid": 2793071, "relation_to_type": "type", "validated": true, "ani": 77.0958, "matched_fragments": 51, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter achroorhodeus", "strain": "strain=MJ1a", "accession": "GCA_007846095.1", "taxid": 2599294, "species_taxid": 2599294, "relation_to_type": "type", "validated": true, "ani": 76.6872, "matched_fragments": 52, "total_fragments": 1551, "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": 76.2286, "matched_fragments": 62, "total_fragments": 1551, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_005116445.1", "gtdb_species": "s__Pedobacter sp005116445", "ani": 100.0, "matched_fragments": 1548, "total_fragments": 1551, "gtdb_taxonomy": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "frigoris" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }