{ "type": "genome", "identifier": "GCF_000410815.1", "organism": "Pedobacter heparinus DSM 2366", "title": "Pedobacter heparinus DSM 2366", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Pacific Biosciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000410815.1", "bioproject": "PRJNA224116", "biosample": "SAMN01909281", "wgs_master": "AQGK00000000.1", "refseq_category": "na", "taxid": "485917", "species_taxid": "984", "organism_name": "Pedobacter heparinus DSM 2366", "infraspecific_name": "strain=DSM 2366", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2013/06/13", "asm_name": "Pedobacter heparinus DSM 2366 HGAP Assembly", "asm_submitter": "Pacific Biosciences", "gbrs_paired_asm": "GCA_000410815.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/410/815/GCF_000410815.1_Pedobacter_heparinus_DSM_2366_HGAP_Assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5171533", "genome_size_ungapped": "5171533", "gc_percent": "42.000000", "replicon_count": "0", "scaffold_count": "3", "contig_count": "3", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000410815.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4295", "protein_coding_gene_count": "4222", "non_coding_gene_count": "69", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2013-06-13", "dateModified": "2013-06-13", "datePublished": "2013-06-13", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter heparinus DSM 2366" ], "sample_taxid": [ "485917" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [], "sample_host_location_id": [], "data_size": "1.458 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)": "5171533", "Number of Sequences": "3", "Longest Sequences (bp)": "2927691", "N50 (bp)": "2927691", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.1", "Number of CDSs": "4205", "Average Protein Length": "376.8", "Coding Ratio (%)": "91.9", "Number of rRNAs": "10", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter heparinus", "strain": "strain=DSM 2366", "accession": "GCA_000410815.1", "taxid": 984, "species_taxid": 984, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1721, "total_fragments": 1722, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter heparinus", "strain": "strain=DSM 2366", "accession": "GCA_000023825.1", "taxid": 984, "species_taxid": 984, "relation_to_type": "type", "validated": true, "ani": 99.9982, "matched_fragments": 1720, "total_fragments": 1722, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter africanus", "strain": "strain=DSM 12126", "accession": "GCA_900176535.1", "taxid": 151894, "species_taxid": 151894, "relation_to_type": "type", "validated": true, "ani": 80.5347, "matched_fragments": 825, "total_fragments": 1722, "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": 80.1014, "matched_fragments": 711, "total_fragments": 1722, "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": 79.8867, "matched_fragments": 658, "total_fragments": 1722, "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": 79.7806, "matched_fragments": 616, "total_fragments": 1722, "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": 79.098, "matched_fragments": 423, "total_fragments": 1722, "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": 79.0283, "matched_fragments": 345, "total_fragments": 1722, "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": 78.7348, "matched_fragments": 427, "total_fragments": 1722, "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": 78.6448, "matched_fragments": 411, "total_fragments": 1722, "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": 77.7433, "matched_fragments": 141, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter aquae", "strain": "strain=CJ43", "accession": "GCA_008195825.1", "taxid": 2605747, "species_taxid": 2605747, "relation_to_type": "type", "validated": true, "ani": 77.48, "matched_fragments": 74, "total_fragments": 1722, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000023825.1", "gtdb_species": "s__Pedobacter heparinus", "ani": 99.9982, "matched_fragments": 1720, "total_fragments": 1722, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", 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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_004331685.1", "gtdb_species": "s__Pedobacter sp004331685", "ani": 79.9193, "matched_fragments": 654, "total_fragments": 1722, "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_900176505.1", "gtdb_species": "s__Pedobacter nyackensis", "ani": 79.7889, "matched_fragments": 615, "total_fragments": 1722, "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", 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"mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000170795.1", "gtdb_species": "s__Pedobacter sp000170795", "ani": 79.1545, "matched_fragments": 311, "total_fragments": 1722, "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_005116445.1", "gtdb_species": "s__Pedobacter sp005116445", "ani": 79.0342, "matched_fragments": 384, "total_fragments": 1722, "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", 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