{ "type": "genome", "identifier": "GCF_004025525.1", "organism": "Pedobacter chitinilyticus", "title": "Pedobacter chitinilyticus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of Sciences", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004025525.1", "bioproject": "PRJNA224116", "biosample": "SAMN09464257", "wgs_master": "SAYW00000000.1", "refseq_category": "reference genome", "taxid": "2233776", "species_taxid": "2233776", "organism_name": "Pedobacter chitinilyticus", "infraspecific_name": "strain=CM134L-2", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/01/15", "asm_name": "ASM402552v1", "asm_submitter": "Chinese Academy of Sciences", "gbrs_paired_asm": "GCA_004025525.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/025/525/GCF_004025525.1_ASM402552v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5052099", "genome_size_ungapped": "5052099", "gc_percent": "39.000000", "replicon_count": "0", "scaffold_count": "10", "contig_count": "10", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004025525.1-RS_2024_10_23", "annotation_date": "2024-10-23", "total_gene_count": "4176", "protein_coding_gene_count": "4117", "non_coding_gene_count": "49", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-01-15", "dateModified": "2019-01-15", "datePublished": "2019-01-15", "_annotation": { "sample_count": 1, "sample_organism": [ "Pedobacter chitinilyticus" ], "sample_taxid": [ "2233776" ], "sample_host_organism": [ "wheat" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Chengdu" ], "sample_host_location_id": [], "data_size": "1.426 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)": "5052099", "Number of Sequences": "10", "Longest Sequences (bp)": "1656356", "N50 (bp)": "611261", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "39.2", "Number of CDSs": "4102", "Average Protein Length": "359.5", "Coding Ratio (%)": "87.6", "Number of rRNAs": "3", "Number of tRNAs": "41", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pedobacter chitinilyticus", "strain": "strain=CM134L-2", "accession": "GCA_004025525.1", "taxid": 2233776, "species_taxid": 2233776, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1679, "total_fragments": 1680, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter chitinilyticus", "strain": "strain=CM134L-2", "accession": "GCA_003313385.1", "taxid": 2233776, "species_taxid": 2233776, "relation_to_type": "type", "validated": true, "ani": 99.9983, "matched_fragments": 1679, "total_fragments": 1680, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pedobacter nanyangensis", "strain": "strain=Q-4", "accession": "GCA_003313505.1", "taxid": 1562389, "species_taxid": 1562389, "relation_to_type": "type", "validated": true, "ani": 84.0575, "matched_fragments": 1066, "total_fragments": 1680, "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": 80.1167, "matched_fragments": 696, "total_fragments": 1680, "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": 80.0177, "matched_fragments": 718, "total_fragments": 1680, "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": 79.9795, "matched_fragments": 721, "total_fragments": 1680, "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": 78.0442, "matched_fragments": 287, "total_fragments": 1680, "ani_threshold": 95, "status": "below_threshold" }, { "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": 77.8908, "matched_fragments": 293, "total_fragments": 1680, "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": 77.6528, "matched_fragments": 210, "total_fragments": 1680, "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": 77.5127, "matched_fragments": 203, "total_fragments": 1680, "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": 77.3, "matched_fragments": 199, "total_fragments": 1680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter gilvus", "strain": "strain=F01003", "accession": "GCA_004054195.1", "taxid": 2305909, "species_taxid": 2305909, "relation_to_type": "type", "validated": true, "ani": 76.56, "matched_fragments": 60, "total_fragments": 1680, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mucilaginibacter robiniae", "strain": "strain=F39-2", "accession": "GCA_012849215.1", "taxid": 2728022, "species_taxid": 2728022, "relation_to_type": "type", "validated": true, "ani": 76.4259, "matched_fragments": 71, "total_fragments": 1680, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003313385.1", "gtdb_species": "s__Pedobacter chitinilyticus", "ani": 99.9983, "matched_fragments": 1679, "total_fragments": 1680, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.94", "min_intra_species_ani": "95.89", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.87", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_003313505.1", "gtdb_species": "s__Pedobacter nanyangensis", "ani": 84.0526, "matched_fragments": 1067, "total_fragments": 1680, "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_005925325.1", "gtdb_species": "s__Pedobacter helvus", "ani": 80.1028, "matched_fragments": 699, "total_fragments": 1680, "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_900215335.1", "gtdb_species": "s__Pedobacter xixiisoli", "ani": 79.9678, "matched_fragments": 723, "total_fragments": 1680, "gtdb_taxonomy": "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": "GCA_002399615.1", "gtdb_species": "s__Pedobacter sp002399615", "ani": 79.6295, 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"total_fragments": 1680, "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_016428855.1", "gtdb_species": "s__Pedobacter sp016428855", "ani": 79.176, "matched_fragments": 504, "total_fragments": 1680, "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_014172375.1", "gtdb_species": "s__Pedobacter planticolens", "ani": 78.0442, "matched_fragments": 287, "total_fragments": 1680, "gtdb_taxonomy": 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