{ "type": "genome", "identifier": "GCF_014648335.1", "organism": "Shewanella litoralis", "title": "Shewanella litoralis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "publication": [ {} ], "properties": { "assembly_accession": "GCF_014648335.1", "bioproject": "PRJNA224116", "biosample": "SAMD00245336", "wgs_master": "BMQX00000000.1", "refseq_category": "reference genome", "taxid": "2282700", "species_taxid": "2282700", "organism_name": "Shewanella litoralis", "infraspecific_name": "strain=JCM 32306", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/09/12", "asm_name": "ASM1464833v1", "asm_submitter": "WFCC-MIRCEN World Data Centre for Microorganisms (WDCM)", "gbrs_paired_asm": "GCA_014648335.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/648/335/GCF_014648335.1_ASM1464833v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4601512", "genome_size_ungapped": "4601351", "gc_percent": "43.000000", "replicon_count": "0", "scaffold_count": "101", "contig_count": "101", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_014648335.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "4052", "protein_coding_gene_count": "3908", "non_coding_gene_count": "99", "pubmed_id": "30832757" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-09-12", "dateModified": "2020-09-12", "datePublished": "2020-09-12", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella litoralis" ], "sample_taxid": [ "2282700" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.309 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 93.75, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4601512", "Number of Sequences": "101", "Longest Sequences (bp)": "384698", "N50 (bp)": "135455", "Gap Ratio (%)": "0.003499", "GCcontent (%)": "42.8", "Number of CDSs": "3944", "Average Protein Length": "331.4", "Coding Ratio (%)": "85.2", "Number of rRNAs": "1", "Number of tRNAs": "86", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella litoralis", "strain": "strain=JCM 32306", "accession": "GCA_014648335.1", "taxid": 2282700, "species_taxid": 2282700, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1487, "total_fragments": 1492, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella litoralis", "strain": "strain=JCM 32306", "accession": "GCA_009828585.1", "taxid": 2282700, "species_taxid": 2282700, "relation_to_type": "type", "validated": true, "ani": 99.9913, "matched_fragments": 1488, "total_fragments": 1492, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella saliphila", "strain": "strain=KCTC 62131", "accession": "GCA_023283695.1", "taxid": 2282698, "species_taxid": 2282698, "relation_to_type": "type", "validated": true, "ani": 88.9523, "matched_fragments": 1192, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella saliphila", "strain": "strain=JCM 32304", "accession": "GCA_014648295.1", "taxid": 2282698, "species_taxid": 2282698, "relation_to_type": "type", "validated": true, "ani": 88.9201, "matched_fragments": 1202, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella algicola", "strain": "strain=JCM 31091", "accession": "GCA_014648035.1", "taxid": 640633, "species_taxid": 640633, "relation_to_type": "type", "validated": true, "ani": 88.8174, "matched_fragments": 1197, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella ulleungensis", "strain": "strain=JCM 32305", "accession": "GCA_014648315.1", "taxid": 2282699, "species_taxid": 2282699, "relation_to_type": "type", "validated": true, "ani": 87.7959, "matched_fragments": 1265, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella ulleungensis", "strain": "strain=KCTC 62130", "accession": "GCA_023283965.1", "taxid": 2282699, "species_taxid": 2282699, "relation_to_type": "type", "validated": true, "ani": 87.7635, "matched_fragments": 1280, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella inventionis", "strain": "strain=KCTC 42807", "accession": "GCA_023283595.1", "taxid": 1738770, "species_taxid": 1738770, "relation_to_type": "type", "validated": true, "ani": 84.8308, "matched_fragments": 1156, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella basaltis", "strain": "strain=KCTC 22121", "accession": "GCA_023283885.1", "taxid": 472183, "species_taxid": 472183, "relation_to_type": "type", "validated": true, "ani": 84.6977, "matched_fragments": 1121, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella vesiculosa", "strain": "strain=M7", "accession": "GCA_021560015.1", "taxid": 518738, "species_taxid": 518738, "relation_to_type": "type", "validated": true, "ani": 81.2245, "matched_fragments": 944, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 93.75, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009828585.1", "gtdb_species": "s__Shewanella litoralis", "ani": 99.9913, "matched_fragments": 1488, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_014648295.1", "gtdb_species": "s__Shewanella saliphila", "ani": 88.9313, "matched_fragments": 1200, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.1181, "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_014648035.1", "gtdb_species": "s__Shewanella algicola", "ani": 88.8052, "matched_fragments": 1199, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.1181, "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_014648315.1", "gtdb_species": "s__Shewanella ulleungensis", "ani": 87.7974, "matched_fragments": 1265, "total_fragments": 1492, "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": "-" }, { "accession": "GCF_014641855.1", "gtdb_species": "s__Shewanella inventionis", "ani": 84.8589, "matched_fragments": 1149, "total_fragments": 1492, "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": "-" }, { "accession": "GCF_003855395.1", "gtdb_species": "s__Shewanella livingstonensis", "ani": 82.0358, "matched_fragments": 1004, "total_fragments": 1492, "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": "-" }, { "accession": "GCF_014164505.1", "gtdb_species": "s__Shewanella sp014164505", "ani": 81.4331, "matched_fragments": 795, "total_fragments": 1492, "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": 22.402, "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", "litoralis" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }