{ "type": "genome", "identifier": "GCF_000722885.1", "organism": "Pedobacter antarcticus 4BY", "title": "Pedobacter antarcticus 4BY", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Centre for Cellular and Molecular Biology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000722885.1", "bioproject": "PRJNA224116", "biosample": "SAMN02777956", "wgs_master": "JNFF00000000.1", "refseq_category": "na", "taxid": "1358423", "species_taxid": "34086", "organism_name": "Pedobacter antarcticus 4BY", "infraspecific_name": "strain=4BY", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/07/07", "asm_name": "ASM72288v1", "asm_submitter": "Centre for Cellular and Molecular Biology", "gbrs_paired_asm": "GCA_000722885.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/722/885/GCF_000722885.1_ASM72288v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4566318", "genome_size_ungapped": "4566318", "gc_percent": "40.500000", "replicon_count": "0", "scaffold_count": "122", "contig_count": "122", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000722885.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4209", "protein_coding_gene_count": "4090", "non_coding_gene_count": "58", "pubmed_id": "25278517" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-07-07", "dateModified": "2014-07-07", "datePublished": "2014-07-07", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter antarcticus 4BY" ], "sample_taxid": [ "1358423" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica: Schirmacher Oasis" ], "sample_host_location_id": [], "data_size": "1.305 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 66.0, "max": 66.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4566318", "Number of Sequences": "122", "Longest Sequences (bp)": "323927", "N50 (bp)": "61879", "Gap Ratio (%)": "0.000066", "GCcontent (%)": "40.4", "Number of CDSs": "4038", "Average Protein Length": "332.2", "Coding Ratio (%)": "88.1", "Number of rRNAs": "3", "Number of tRNAs": "48", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter antarcticus", "strain": "strain=4BY", "accession": "GCA_000722885.1", "taxid": 34086, "species_taxid": 34086, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1457, "total_fragments": 1463, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter antarcticus", "strain": "strain=ATCC 51969", "accession": "GCA_900112985.1", "taxid": 34086, "species_taxid": 34086, "relation_to_type": "type", "validated": true, "ani": 99.9847, "matched_fragments": 1462, "total_fragments": 1463, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter hartonius", "strain": "strain=DSM 19033", "accession": "GCA_900107535.1", "taxid": 425514, "species_taxid": 425514, "relation_to_type": "type", "validated": true, "ani": 79.4395, "matched_fragments": 274, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter lusitanus", "strain": "strain=NL19", "accession": "GCA_000832545.1", "taxid": 1503925, "species_taxid": 1503925, "relation_to_type": "type", "validated": true, "ani": 79.2157, "matched_fragments": 360, "total_fragments": 1463, "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": 79.1765, "matched_fragments": 356, "total_fragments": 1463, "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": 78.9816, "matched_fragments": 300, "total_fragments": 1463, "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": 77.9993, "matched_fragments": 204, "total_fragments": 1463, "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": 77.981, "matched_fragments": 203, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter nutrimenti", "strain": "strain=DSM 27372", "accession": "GCA_003208655.1", "taxid": 1241337, "species_taxid": 1241337, "relation_to_type": "type", "validated": true, "ani": 77.9348, "matched_fragments": 209, "total_fragments": 1463, "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": 77.7875, "matched_fragments": 172, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter endophyticus", "strain": "strain=JBR3-12", "accession": "GCA_015679185.1", "taxid": 2789740, "species_taxid": 2789740, "relation_to_type": "type", "validated": true, "ani": 77.6844, "matched_fragments": 97, "total_fragments": 1463, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900112985.1", "gtdb_species": "s__Pedobacter antarcticus", "ani": 99.9847, "matched_fragments": 1462, "total_fragments": 1463, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.39", "min_intra_species_ani": "98.80", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCA_014302835.1", "gtdb_species": "s__Pedobacter sp014302835", "ani": 79.5011, "matched_fragments": 281, 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"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_000832545.1", "gtdb_species": "s__Pedobacter lusitanus", "ani": 79.1721, "matched_fragments": 362, "total_fragments": 1463, "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_003259615.1", "gtdb_species": "s__Pedobacter cryoconitis", "ani": 79.1713, "matched_fragments": 355, "total_fragments": 1463, "gtdb_taxonomy": 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"d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.76", "min_intra_species_ani": "98.76", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.93", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000170795.1", "gtdb_species": "s__Pedobacter sp000170795", "ani": 79.0396, "matched_fragments": 180, "total_fragments": 1463, "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_900182595.1", "gtdb_species": "s__Pedobacter westerhofensis", "ani": 78.9989, "matched_fragments": 298, "total_fragments": 1463, "gtdb_taxonomy": 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"vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Pedobacter", "antarcticus", "4BY" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }