{ "type": "genome", "identifier": "GCF_002836975.1", "organism": "Shewanella indica", "title": "Shewanella indica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute for Communicable Disease Control and Prevention, China CDC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002836975.1", "bioproject": "PRJNA224116", "biosample": "SAMN07175133", "wgs_master": "NIJK00000000.1", "refseq_category": "na", "taxid": "768528", "species_taxid": "768528", "organism_name": "Shewanella indica", "infraspecific_name": "strain=KJW27", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/12/12", "asm_name": "ASM283697v1", "asm_submitter": "National Institute for Communicable Disease Control and Prevention, China CDC", "gbrs_paired_asm": "GCA_002836975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/836/975/GCF_002836975.1_ASM283697v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4402806", "genome_size_ungapped": "4402680", "gc_percent": "52.500000", "replicon_count": "0", "scaffold_count": "55", "contig_count": "55", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002836975.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "3981", "protein_coding_gene_count": "3806", "non_coding_gene_count": "118", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-12-12", "dateModified": "2017-12-12", "datePublished": "2017-12-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella indica" ], "sample_taxid": [ "768528" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not collected" ], "sample_host_location_id": [], "data_size": "1.252 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)": "4402806", "Number of Sequences": "55", "Longest Sequences (bp)": "382256", "N50 (bp)": "129838", "Gap Ratio (%)": "0.003793", "GCcontent (%)": "52.4", "Number of CDSs": "3891", "Average Protein Length": "325.6", "Coding Ratio (%)": "86.3", "Number of rRNAs": "3", "Number of tRNAs": "108", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella indica", "strain": "strain=KJW27", "accession": "GCA_002836975.1", "taxid": 768528, "species_taxid": 768528, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1437, "total_fragments": 1439, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella indica", "strain": "strain=KCTC 23171", "accession": "GCA_014652115.1", "taxid": 768528, "species_taxid": 768528, "relation_to_type": "type", "validated": true, "ani": 99.9911, "matched_fragments": 1423, "total_fragments": 1439, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=JC5", "accession": "GCA_003217175.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 95.8024, "matched_fragments": 1307, "total_fragments": 1439, "ani_threshold": 95, "status": "inconclusive" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=KCTC 22540", "accession": "GCA_014651975.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 95.7851, 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"status": "below_threshold" }, { "organism_name": "Shewanella algae", "strain": "strain=NBRC 103173", "accession": "GCA_001598875.1", "taxid": 38313, "species_taxid": 38313, "relation_to_type": "type", "validated": true, "ani": 94.2539, "matched_fragments": 1254, "total_fragments": 1439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella algae", "strain": "strain=CECT 5071", "accession": "GCA_009183365.2", "taxid": 38313, "species_taxid": 38313, "relation_to_type": "type", "validated": true, "ani": 94.2373, "matched_fragments": 1307, "total_fragments": 1439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella carassii", "strain": "strain=CGMCC 1.16033", "accession": "GCA_014644375.1", "taxid": 1987584, "species_taxid": 1987584, "relation_to_type": "type", "validated": true, "ani": 93.7332, "matched_fragments": 1247, "total_fragments": 1439, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000016065.1", "gtdb_species": "s__Shewanella loihica", "ani": 78.1025, "matched_fragments": 426, "total_fragments": 1439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.22", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.91", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_018394335.1", "gtdb_species": "s__Shewanella dokdonensis", "ani": 77.9765, "matched_fragments": 251, "total_fragments": 1439, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "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": -0.227, "cell_length": 0.265, "doubling_h": 0.077, "growth_tmp": 37.0, "optimum_tmp": 22.248, "optimum_ph": 7.147, "genome_size": 4868941.65, "gc_content": 46.142, "coding_genes": 4161.776, "rRNA16S_genes": 9.437, "tRNA_genes": 107.731, "gram_stain": 0.0, "sporulation": 0.0, "motility": 1.0, "range_salinity": 0.333, "facultative_respiration": 0.565, "anaerobic_respiration": 0.021, "aerobic_respiration": 0.413, "mesophilic_range_tmp": 0.812, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.187, "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": [ "Shewanella", "indica" ], "quality": 4, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }