{ "type": "genome", "identifier": "GCF_009758125.1", "organism": "Chitinophaga oryziterrae", "title": "Chitinophaga oryziterrae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Guangdong Institute of Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009758125.1", "bioproject": "PRJNA224116", "biosample": "SAMN13509244", "wgs_master": "WRXO00000000.1", "refseq_category": "reference genome", "taxid": "1031224", "species_taxid": "1031224", "organism_name": "Chitinophaga oryziterrae", "infraspecific_name": "strain=JCM 16595", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/12/17", "asm_name": "ASM975812v1", "asm_submitter": "Guangdong Institute of Microbiology", "gbrs_paired_asm": "GCA_009758125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/758/125/GCF_009758125.1_ASM975812v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "8109716", "genome_size_ungapped": "8109716", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "44", "contig_count": "44", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009758125.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "6378", "protein_coding_gene_count": "6307", "non_coding_gene_count": "60", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-12-17", "dateModified": "2019-12-17", "datePublished": "2019-12-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Chitinophaga oryziterrae" ], "sample_taxid": [ "1031224" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "South Korea: Jinju" ], "sample_host_location_id": [], "data_size": "2.300 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)": "8109716", "Number of Sequences": "44", "Longest Sequences (bp)": "1836206", "N50 (bp)": "656932", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.1", "Number of CDSs": "6274", "Average Protein Length": "378.7", "Coding Ratio (%)": "87.9", "Number of rRNAs": "5", "Number of tRNAs": "50", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Chitinophaga oryziterrae", "strain": "strain=JCM 16595", "accession": "GCA_009758125.1", "taxid": 1031224, "species_taxid": 1031224, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 2681, "total_fragments": 2684, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Chitinophaga ginsengisoli", "strain": "strain=DSM 18107", "accession": "GCA_003014595.1", "taxid": 363837, "species_taxid": 363837, "relation_to_type": "type", "validated": true, "ani": 78.9536, "matched_fragments": 791, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga tropicalis", "strain": "strain=ysch24", "accession": "GCA_009758205.1", "taxid": 2683588, "species_taxid": 2683588, "relation_to_type": "type", "validated": true, "ani": 78.898, "matched_fragments": 743, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga filiformis", "strain": "strain=DSM 527", "accession": "GCA_900102545.1", "taxid": 104663, "species_taxid": 104663, "relation_to_type": "type", "validated": true, "ani": 78.7291, "matched_fragments": 794, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga pinensis", "strain": "strain=DSM 2588", "accession": "GCA_000024005.1", "taxid": 79329, "species_taxid": 79329, "relation_to_type": "type", "validated": true, "ani": 78.6199, "matched_fragments": 706, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga silvisoli", "strain": "strain=K20C18050901", "accession": "GCA_003412465.1", "taxid": 2291814, "species_taxid": 2291814, "relation_to_type": "type", "validated": true, "ani": 78.5767, "matched_fragments": 602, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga agri", "strain": "strain=H33E-04", "accession": "GCA_010093065.1", "taxid": 2703787, "species_taxid": 2703787, "relation_to_type": "type", "validated": true, "ani": 78.4995, "matched_fragments": 624, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga sancti", "strain": "strain=DSM 784", "accession": "GCA_900119105.1", "taxid": 1004, "species_taxid": 1004, "relation_to_type": "type", "validated": true, "ani": 78.3313, "matched_fragments": 614, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga fulva", "strain": "strain=G-6-1-13", "accession": "GCA_012927205.1", "taxid": 2728842, "species_taxid": 2728842, "relation_to_type": "type", "validated": true, "ani": 77.5208, "matched_fragments": 310, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chitinophaga hostae", "strain": "strain=2R12", "accession": "GCA_018224885.1", "taxid": 2831022, "species_taxid": 2831022, "relation_to_type": "type", "validated": true, "ani": 77.4874, "matched_fragments": 344, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Filimonas lacunae", "strain": "strain=DSM 21054", "accession": "GCA_900156765.1", "taxid": 477680, "species_taxid": 477680, "relation_to_type": "type", "validated": true, "ani": 75.7671, "matched_fragments": 88, "total_fragments": 2684, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009758125.1", "gtdb_species": "s__Chitinophaga oryziterrae", "ani": 100.0, "matched_fragments": 2681, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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": "conclusive" }, { "accession": "GCF_900110995.1", "gtdb_species": "s__Chitinophaga sp900110995", "ani": 90.9674, "matched_fragments": 2035, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900112615.1", "gtdb_species": "s__Chitinophaga sp900112615", "ani": 82.3684, "matched_fragments": 1499, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900142925.1", "gtdb_species": "s__Chitinophaga sp900142925", "ani": 79.1325, "matched_fragments": 759, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_003014595.1", "gtdb_species": "s__Chitinophaga ginsengisoli", "ani": 78.94, "matched_fragments": 793, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_009758205.1", "gtdb_species": "s__Chitinophaga sp009758205", "ani": 78.8924, "matched_fragments": 743, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_001975825.1", "gtdb_species": "s__Chitinophaga sp001975825", "ani": 78.8443, "matched_fragments": 657, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.88", "min_intra_species_ani": "98.88", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003182155.1", "gtdb_species": "s__Chitinophaga sp003182155", "ani": 78.763, "matched_fragments": 714, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900102545.1", "gtdb_species": "s__Chitinophaga filiformis", "ani": 78.7313, "matched_fragments": 793, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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": "GCA_902168105.1", "gtdb_species": "s__Chitinophaga sp902168105", "ani": 78.6043, "matched_fragments": 695, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_900119105.1", "gtdb_species": "s__Chitinophaga sancti", "ani": 78.3313, "matched_fragments": 614, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_019091455.1", "gtdb_species": "s__Chitinophaga sp019091455", "ani": 77.5814, "matched_fragments": 447, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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_012927205.1", "gtdb_species": "s__Chitinophaga fulva", "ani": 77.5242, "matched_fragments": 309, "total_fragments": 2684, "gtdb_taxonomy": "d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga", "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": -0.456, "cell_length": 0.612, "doubling_h": null, "growth_tmp": 28.733, "optimum_tmp": 27.5, "optimum_ph": 7.0, "genome_size": 7579043.287, "gc_content": 45.2, "coding_genes": 7126.333, "rRNA16S_genes": 6.0, "tRNA_genes": 72.0, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": null, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Chitinophaga", "oryziterrae" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }