{ "type": "genome", "identifier": "GCF_003315595.1", "organism": "Pedobacter miscanthi", "title": "Pedobacter miscanthi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Hubei University of Arts and Science", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003315595.1", "bioproject": "PRJNA224116", "biosample": "SAMN09531634", "wgs_master": "QNQU00000000.1", "refseq_category": "reference genome", "taxid": "2259170", "species_taxid": "2259170", "organism_name": "Pedobacter miscanthi", "infraspecific_name": "strain=RS10", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/07/12", "asm_name": "ASM331559v1", "asm_submitter": "Hubei University of Arts and Science", "gbrs_paired_asm": "GCA_003315595.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/315/595/GCF_003315595.1_ASM331559v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6696979", "genome_size_ungapped": "6696916", "gc_percent": "39.500000", "replicon_count": "0", "scaffold_count": "100", "contig_count": "100", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003315595.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "5618", "protein_coding_gene_count": "5540", "non_coding_gene_count": "61", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-07-12", "dateModified": "2018-07-12", "datePublished": "2018-07-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter miscanthi" ], "sample_taxid": [ "2259170" ], "sample_host_organism": [ "Chinese silvergrass" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China" ], "sample_host_location_id": [], "data_size": "1.886 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)": "6696979", "Number of Sequences": "100", "Longest Sequences (bp)": "475104", "N50 (bp)": "224538", "Gap Ratio (%)": "0.001389", "GCcontent (%)": "39.7", "Number of CDSs": "5469", "Average Protein Length": "338.5", "Coding Ratio (%)": "82.9", "Number of rRNAs": "2", "Number of tRNAs": "48", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter miscanthi", "strain": "strain=RS10", "accession": "GCA_003315595.1", "taxid": 2259170, "species_taxid": 2259170, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2191, "total_fragments": 2194, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter borealis", "strain": "strain=DSM 19626", "accession": "GCA_000708285.2", "taxid": 475254, "species_taxid": 475254, "relation_to_type": "type", "validated": true, "ani": 83.1658, "matched_fragments": 1027, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_003664035.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 83.1359, "matched_fragments": 1156, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter zeae", "strain": "strain=CGMCC 1.15287", "accession": "GCA_014641575.1", "taxid": 1737356, "species_taxid": 1737356, "relation_to_type": "type", "validated": true, "ani": 83.0689, "matched_fragments": 1155, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter alluvionis", "strain": "strain=DSM 19624", "accession": "GCA_004402005.1", "taxid": 475253, "species_taxid": 475253, "relation_to_type": "type", "validated": true, "ani": 83.0642, "matched_fragments": 1149, "total_fragments": 2194, "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": 82.9939, "matched_fragments": 1221, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter zeae", "strain": "strain=DSM 100774", "accession": "GCA_014196715.1", "taxid": 1737356, "species_taxid": 1737356, "relation_to_type": "type", "validated": true, "ani": 82.9789, "matched_fragments": 1152, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "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": 82.978, "matched_fragments": 1184, "total_fragments": 2194, "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", "validated": true, "ani": 82.7326, "matched_fragments": 1196, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter terrae", "strain": "strain=DSM 17933", "accession": "GCA_900100705.1", "taxid": 405671, "species_taxid": 405671, "relation_to_type": "type", "validated": true, "ani": 82.5248, "matched_fragments": 1073, "total_fragments": 2194, "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": 81.771, "matched_fragments": 1056, "total_fragments": 2194, "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": 79.8038, "matched_fragments": 748, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pedobacter mucosus", "strain": "strain=Q8-18", "accession": "GCA_022200785.1", "taxid": 2895286, "species_taxid": 2895286, "relation_to_type": "type", "validated": true, "ani": 78.7532, "matched_fragments": 544, "total_fragments": 2194, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter agri", "strain": "strain=R11", "accession": "GCA_009928685.1", "taxid": 2695265, 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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_000633455.1", "gtdb_species": "s__Pedobacter jeongneungensis", "ani": 85.133, "matched_fragments": 1443, "total_fragments": 2194, "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_014395225.1", "gtdb_species": "s__Pedobacter roseus", "ani": 84.994, "matched_fragments": 1444, "total_fragments": 2194, "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": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900100705.1", "gtdb_species": "s__Pedobacter terrae", "ani": 82.5463, "matched_fragments": 1069, "total_fragments": 2194, "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": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.28, "cell_length": 0.284, "doubling_h": null, "growth_tmp": 24.703, "optimum_tmp": 25.616, "optimum_ph": 7.026, "genome_size": 5519163.389, 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