{ "type": "genome", "identifier": "GCF_001976145.1", "organism": "Serratia oryzae", "title": "Serratia oryzae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of agricultural Sciences(CAAS)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_001976145.1", "bioproject": "PRJNA224116", "biosample": "SAMN05970538", "wgs_master": "MOXD00000000.1", "refseq_category": "reference genome", "taxid": "2034155", "species_taxid": "2034155", "organism_name": "Serratia oryzae", "infraspecific_name": "strain=J11-6", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/01/31", "asm_name": "ASM197614v1", "asm_submitter": "Chinese Academy of agricultural Sciences(CAAS)", "gbrs_paired_asm": "GCA_001976145.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/976/145/GCF_001976145.1_ASM197614v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5012778", "genome_size_ungapped": "5012012", "gc_percent": "53.000000", "replicon_count": "0", "scaffold_count": "81", "contig_count": "81", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_001976145.1-RS_2024_04_22", "annotation_date": "2024-04-22", "total_gene_count": "4577", "protein_coding_gene_count": "4376", "non_coding_gene_count": "95", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-01-31", "dateModified": "2017-01-31", "datePublished": "2017-01-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Serratia oryzae" ], "sample_taxid": [ "2034155" ], "sample_host_organism": [ "rice" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Hunan" ], "sample_host_location_id": [], "data_size": "1.424 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 30.0, "max": 30.0 }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5012778", "Number of Sequences": "81", "Longest Sequences (bp)": "676451", "N50 (bp)": "368300", "Gap Ratio (%)": "0.015281", "GCcontent (%)": "53.2", "Number of CDSs": "4414", "Average Protein Length": "318.2", "Coding Ratio (%)": "84.1", "Number of rRNAs": "2", "Number of tRNAs": "73", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Chania multitudinisentens", "strain": "strain=RB-25", "accession": "GCA_000568195.1", "taxid": 1639108, "species_taxid": 1639108, "relation_to_type": "type", "validated": true, "ani": 84.1569, "matched_fragments": 1111, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chania multitudinisentens", "strain": "strain=RB-25", "accession": "GCA_000520015.2", "taxid": 1639108, "species_taxid": 1639108, "relation_to_type": "type", "validated": true, "ani": 84.0821, "matched_fragments": 1134, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia fonticola", "strain": "strain=LMG 7882", "accession": "GCA_000469035.1", "taxid": 47917, "species_taxid": 47917, "relation_to_type": "suspected-type", "validated": true, "ani": 83.4328, "matched_fragments": 978, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia fonticola", "strain": "strain=DSM 4576", "accession": "GCA_001006005.1", "taxid": 47917, "species_taxid": 47917, "relation_to_type": "suspected-type", "validated": true, "ani": 83.3985, "matched_fragments": 1040, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia entomophila", "strain": "strain=A1", "accession": "GCA_021462285.1", "taxid": 42906, "species_taxid": 42906, "relation_to_type": "type", "validated": true, "ani": 82.9099, "matched_fragments": 893, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia plymuthica", "strain": "strain=FDAARGOS_895", "accession": "GCA_016027675.1", "taxid": 82996, "species_taxid": 82996, "relation_to_type": "type", "validated": true, "ani": 82.6638, "matched_fragments": 914, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia liquefaciens", "strain": "strain=ATCC 27592", "accession": "GCA_000422085.1", "taxid": 614, "species_taxid": 614, "relation_to_type": "type", "validated": true, "ani": 82.5696, "matched_fragments": 899, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia proteamaculans", "strain": "strain=CCUG 14510", "accession": "GCA_008830365.1", "taxid": 28151, "species_taxid": 28151, "relation_to_type": "type", "validated": true, "ani": 82.4398, "matched_fragments": 900, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia nevei", "strain": "strain=S15", "accession": "GCA_008364245.1", "taxid": 2703794, "species_taxid": 2703794, "relation_to_type": "type", "validated": true, "ani": 82.368, "matched_fragments": 901, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia marcescens", "strain": "strain=ATCC 13880", "accession": "GCA_017654245.1", "taxid": 615, "species_taxid": 615, "relation_to_type": "suspected-type", "validated": true, "ani": 82.3458, "matched_fragments": 912, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia ureilytica", "strain": "strain=CCUG:50595", "accession": "GCA_013375155.1", "taxid": 300181, "species_taxid": 300181, "relation_to_type": "type", "validated": true, "ani": 82.3004, "matched_fragments": 895, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia quinivorans", "strain": "strain=NCTC11544", "accession": "GCA_900457075.1", "taxid": 137545, "species_taxid": 137545, "relation_to_type": "suspected-type", "validated": true, "ani": 82.265, "matched_fragments": 924, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia surfactantfaciens", "strain": "strain=YD25", "accession": "GCA_001642805.2", "taxid": 2741499, "species_taxid": 2741499, "relation_to_type": "type", "validated": true, "ani": 82.2489, "matched_fragments": 899, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia bockelmannii", "strain": "strain=S3", "accession": "GCA_008011855.1", "taxid": 2703793, "species_taxid": 2703793, "relation_to_type": "type", "validated": true, "ani": 82.2167, "matched_fragments": 877, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia odorifera", "strain": "strain=NCTC11214", "accession": "GCA_900635445.1", "taxid": 618, "species_taxid": 618, "relation_to_type": "type", "validated": true, "ani": 81.8431, "matched_fragments": 832, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia grimesii", "strain": "strain=NCTC11543", "accession": "GCA_900456935.1", "taxid": 82995, "species_taxid": 82995, "relation_to_type": "type", "validated": true, "ani": 81.6723, "matched_fragments": 858, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Serratia grimesii", "strain": "strain=NBRC 13537", "accession": "GCA_001590905.1", "taxid": 82995, "species_taxid": 82995, "relation_to_type": "type", "validated": true, "ani": 81.6666, "matched_fragments": 840, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella bonaserana", "strain": "strain=H11b", "accession": "GCA_019049675.1", "taxid": 2816248, "species_taxid": 2816248, "relation_to_type": "type", "validated": true, "ani": 79.1205, "matched_fragments": 486, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella perminowiae", "strain": "strain=SL6", "accession": "GCA_019049755.1", "taxid": 2816244, "species_taxid": 2816244, "relation_to_type": "type", "validated": true, "ani": 79.079, "matched_fragments": 439, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella grimontii", "strain": "strain=06D021", "accession": "GCA_900200035.1", "taxid": 2058152, "species_taxid": 2058152, "relation_to_type": "type", "validated": true, "ani": 78.573, "matched_fragments": 433, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella pasteurii", "strain": "", "accession": "GCA_902158725.1", "taxid": 2587529, "species_taxid": 2587529, "relation_to_type": "type", "validated": true, "ani": 78.2558, "matched_fragments": 450, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Photorhabdus heterorhabditis subsp. aluminescens", "strain": "strain=Q614", "accession": "GCA_013277735.1", "taxid": 2805094, "species_taxid": 880156, "relation_to_type": "type", "validated": true, "ani": 78.0636, "matched_fragments": 145, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sodalis ligni", "strain": "strain=159R", "accession": "GCA_004346745.1", "taxid": 2697027, "species_taxid": 2697027, "relation_to_type": "type", "validated": true, "ani": 77.5335, "matched_fragments": 329, "total_fragments": 1641, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_001976145.1", "gtdb_species": "s__Chania oryzae", "ani": 100.0, "matched_fragments": 1641, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.90", "min_intra_species_ani": "98.79", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000743355.1", "gtdb_species": "s__Chania sp000743355", "ani": 86.8278, "matched_fragments": 1277, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.97", "min_intra_species_ani": "99.97", "mean_intra_species_af": "0.98", "min_intra_species_af": "0.98", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000520015.2", "gtdb_species": "s__Chania multitudinisentens", "ani": 84.1013, "matched_fragments": 1131, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Chania", "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_001006005.1", "gtdb_species": "s__Serratia_A fonticola", "ani": 83.394, "matched_fragments": 1041, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.10", "min_intra_species_ani": "95.03", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.81", "num_clustered_genomes": 45, "status": "-" }, { "accession": "GCF_000633355.1", "gtdb_species": "s__Serratia_A sp000633355", "ani": 83.3166, "matched_fragments": 1030, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A", "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_006715025.1", "gtdb_species": "s__Serratia_A fonticola_A", "ani": 83.1265, "matched_fragments": 1028, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A", "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": 4, "status": "-" }, { "accession": "GCF_018336935.1", "gtdb_species": "s__Serratia plymuthica_B", "ani": 82.7548, "matched_fragments": 915, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "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_000422085.1", "gtdb_species": "s__Serratia liquefaciens", "ani": 82.5601, "matched_fragments": 899, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.63", "min_intra_species_ani": "98.20", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_016742975.1", "gtdb_species": "s__Serratia nevei", "ani": 82.3789, "matched_fragments": 805, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "ani_circumscription_radius": 96.1913, "mean_intra_species_ani": "97.82", "min_intra_species_ani": "96.26", "mean_intra_species_af": "0.83", "min_intra_species_af": "0.75", "num_clustered_genomes": 139, "status": "-" }, { "accession": "GCF_002220655.1", "gtdb_species": "s__Serratia marcescens_K", "ani": 82.343, "matched_fragments": 920, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "ani_circumscription_radius": 96.0833, "mean_intra_species_ani": "98.79", "min_intra_species_ani": "98.10", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 411, "status": "-" }, { "accession": "GCF_006715005.1", "gtdb_species": "s__Serratia marcescens_J", "ani": 82.2922, "matched_fragments": 899, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "ani_circumscription_radius": 96.1913, "mean_intra_species_ani": "98.92", "min_intra_species_ani": "98.92", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.95", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001642805.2", "gtdb_species": "s__Serratia surfactantfaciens", "ani": 82.2489, "matched_fragments": 899, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.81", "min_intra_species_ani": "97.95", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 10, "status": "-" }, { "accession": "GCF_000496755.2", "gtdb_species": "s__Serratia_A sp000496755", "ani": 80.1043, "matched_fragments": 697, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Serratia_A", "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_009831415.1", "gtdb_species": "s__Yersinia canariae", "ani": 79.3122, "matched_fragments": 445, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.93", "min_intra_species_ani": "98.81", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000770305.1", "gtdb_species": "s__Erwinia oleae", "ani": 78.2004, "matched_fragments": 366, "total_fragments": 1641, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.06", "min_intra_species_ani": "98.06", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.89", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": -0.158, "cell_length": 0.113, "doubling_h": -0.246, "growth_tmp": 29.567, "optimum_tmp": 28.433, "optimum_ph": 7.172, "genome_size": 5022862.929, "gc_content": 52.905, "coding_genes": 4316.522, "rRNA16S_genes": 7.095, "tRNA_genes": 77.398, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "facultative_respiration": 0.4, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.6, "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": [ "Serratia", "oryzae" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }