{ "type": "genome", "identifier": "GCA_004211475.1", "organism": "Pedobacter sp.", "title": "Pedobacter sp.", "description": "derived from metagenome; fragmented assembly", "data type": "Genome sequencing and assembly", "organization": "University of East Anglia", "publication": [ {} ], "properties": { "assembly_accession": "GCA_004211475.1", "bioproject": "PRJNA272922", "biosample": "SAMN10678637", "wgs_master": "SEDP00000000.1", "refseq_category": "na", "taxid": "1411316", "species_taxid": "1411316", "organism_name": "Pedobacter sp.", "infraspecific_name": "", "isolate": "PMG_224", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/02/19", "asm_name": "ASM421147v1", "submitter": "University of East Anglia", "gbrs_paired_asm": "na", "paired_asm_comp": "na", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/004/211/475/GCA_004211475.1_ASM421147v1", "excluded_from_refseq": "derived from metagenome; fragmented assembly", "relation_to_type_material": "", "asm_not_live_date": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-02-19", "dateModified": "2019-02-19", "datePublished": "2019-02-19", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter sp." ], "sample_taxid": [ "1411316" ], "sample_host_organism": [ "Populus alba" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "United Kingdom: Norwich" ], "sample_host_location_id": [], "data_size": "2.118 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 87.12, "contamination": 59.9, "strain_heterogeneity": 23.08, "genome_count": 1 }, "data_type": "MAG", "data_source": "INSDC", "_dfast": { "Total Sequence Length (bp)": "7435257", "Number of Sequences": "2466", "Longest Sequences (bp)": "51834", "N50 (bp)": "4524", "Gap Ratio (%)": "0.000538", "GCcontent (%)": "34.6", "Number of CDSs": "4993", "Average Protein Length": "294.5", "Coding Ratio (%)": "59.3", "Number of rRNAs": "0", "Number of tRNAs": "62", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter polaris", "strain": "strain=RP-3-22", "accession": "GCA_005116505.1", "taxid": 2571273, "species_taxid": 2571273, "relation_to_type": "type", "validated": true, "ani": 80.5322, "matched_fragments": 593, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter cryotolerans", "strain": "strain=AR-2-6", "accession": "GCA_005116475.1", "taxid": 2571270, "species_taxid": 2571270, "relation_to_type": "type", "validated": true, "ani": 80.4911, "matched_fragments": 565, "total_fragments": 1237, "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": 79.9884, "matched_fragments": 559, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter planticolens", "strain": "strain=LMG 31464", "accession": "GCA_014172375.1", "taxid": 2679964, "species_taxid": 2679964, "relation_to_type": "type", "validated": true, "ani": 79.4346, "matched_fragments": 488, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter namyangjuensis", "strain": "strain=5G38", "accession": "GCA_003313325.1", "taxid": 600626, "species_taxid": 600626, "relation_to_type": "type", "validated": true, "ani": 78.6129, "matched_fragments": 401, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter insulae", "strain": "strain=DSM 18684", "accession": "GCA_900113525.1", "taxid": 414048, "species_taxid": 414048, "relation_to_type": "type", "validated": true, "ani": 77.8048, "matched_fragments": 219, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter xixiisoli", "strain": "strain=S27", "accession": "GCA_005925365.1", "taxid": 1476464, "species_taxid": 1476464, "relation_to_type": "type", "validated": true, "ani": 77.2342, "matched_fragments": 230, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter frigidisoli", "strain": "strain=RP-3-11", "accession": "GCA_004331675.1", "taxid": 2530455, "species_taxid": 2530455, "relation_to_type": "type", "validated": true, "ani": 77.2121, "matched_fragments": 220, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter xixiisoli", "strain": "strain=CGMCC 1.12803", "accession": "GCA_900215335.1", "taxid": 1476464, "species_taxid": 1476464, "relation_to_type": "type", "validated": true, "ani": 77.2044, "matched_fragments": 233, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter fastidiosus", "strain": "strain=CCM 8938", "accession": "GCA_014306625.1", "taxid": 2765361, "species_taxid": 2765361, "relation_to_type": "type", "validated": true, "ani": 77.1415, "matched_fragments": 223, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter yonginense", "strain": "strain=KCTC22721", "accession": "GCA_003173595.1", "taxid": 651869, "species_taxid": 651869, "relation_to_type": "type", "validated": true, "ani": 76.9257, "matched_fragments": 172, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter helvus", "strain": "strain=P-25", "accession": "GCA_005925325.1", "taxid": 2563444, "species_taxid": 2563444, "relation_to_type": "type", "validated": true, "ani": 76.8944, "matched_fragments": 209, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter agri", "strain": "strain=PB92", "accession": "GCA_000258495.1", "taxid": 454586, "species_taxid": 454586, "relation_to_type": "type", "validated": true, "ani": 76.7658, "matched_fragments": 181, "total_fragments": 1237, "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": 76.6323, "matched_fragments": 185, "total_fragments": 1237, "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": 76.4119, "matched_fragments": 106, "total_fragments": 1237, "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": 76.387, "matched_fragments": 128, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" }, { "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": 76.2997, "matched_fragments": 93, "total_fragments": 1237, "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": 76.2222, "matched_fragments": 87, "total_fragments": 1237, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 87.12, "contamination": 59.9, "strain_heterogeneity": 23.08 }, "gtdb_result": [ { "accession": "GCF_005116505.1", "gtdb_species": "s__Pedobacter sp005116505", "ani": 80.5358, "matched_fragments": 593, "total_fragments": 1237, "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_005116475.1", "gtdb_species": "s__Pedobacter sp005116475", "ani": 80.4807, "matched_fragments": 566, "total_fragments": 1237, "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": "-" 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