{ "type": "genome", "identifier": "GCF_023283945.1", "organism": "Shewanella gelidimarina", "title": "Shewanella gelidimarina", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Karolinska Institutet", "publication": [ {} ], "properties": { "assembly_accession": "GCF_023283945.1", "bioproject": "PRJNA224116", "biosample": "SAMN24537870", "wgs_master": "JAKIKW000000000.1", "refseq_category": "reference genome", "taxid": "56813", "species_taxid": "56813", "organism_name": "Shewanella gelidimarina", "infraspecific_name": "strain=ATCC 700752", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2022/05/09", "asm_name": "ASM2328394v1", "asm_submitter": "Karolinska Institutet", "gbrs_paired_asm": "GCA_023283945.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/023/283/945/GCF_023283945.1_ASM2328394v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5033801", "genome_size_ungapped": "5033801", "gc_percent": "43.500000", "replicon_count": "0", "scaffold_count": "79", "contig_count": "79", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_023283945.1-RS_2024_05_18", "annotation_date": "2024-05-18", "total_gene_count": "4328", "protein_coding_gene_count": "4169", "non_coding_gene_count": "114", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2022-05-09", "dateModified": "2022-05-09", "datePublished": "2022-05-09", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella gelidimarina" ], "sample_taxid": [ "56813" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Antarctica: Prydz Bay" ], "sample_host_location_id": [], "data_size": "1.439 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)": "5033801", "Number of Sequences": "79", "Longest Sequences (bp)": "439870", "N50 (bp)": "148847", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "43.6", "Number of CDSs": "4216", "Average Protein Length": "330.0", "Coding Ratio (%)": "82.9", "Number of rRNAs": "2", "Number of tRNAs": "94", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella gelidimarina", "strain": "strain=ATCC 700752", "accession": "GCA_023283945.1", "taxid": 56813, "species_taxid": 56813, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1636, "total_fragments": 1640, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Shewanella abyssi", "strain": "strain=DSM 17171", "accession": "GCA_023284025.1", "taxid": 311789, "species_taxid": 311789, "relation_to_type": "type", "validated": true, "ani": 85.1142, "matched_fragments": 1198, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella kaireitica", "strain": "strain=DSM 17170", "accession": "GCA_023284045.1", "taxid": 212021, "species_taxid": 212021, "relation_to_type": "type", "validated": true, "ani": 81.657, "matched_fragments": 946, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella piezotolerans", "strain": "strain=WP3", "accession": "GCA_000014885.1", "taxid": 404011, "species_taxid": 404011, "relation_to_type": "type", "validated": true, "ani": 81.3209, "matched_fragments": 959, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella pealeana", "strain": "strain=ATCC 700345", "accession": "GCA_000018285.1", "taxid": 70864, "species_taxid": 70864, "relation_to_type": "type", "validated": true, "ani": 79.8667, "matched_fragments": 592, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella sairae", "strain": "strain=JCM 11563", "accession": "GCA_019655015.1", "taxid": 190310, "species_taxid": 190310, "relation_to_type": "type", "validated": true, "ani": 79.6744, "matched_fragments": 589, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella marinintestina", "strain": "strain=LMG 21403", "accession": "GCA_023283845.1", "taxid": 190305, "species_taxid": 190305, "relation_to_type": "type", "validated": true, "ani": 79.5694, "matched_fragments": 609, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella sairae", "strain": "strain=LMG 21408", "accession": "GCA_023283535.1", "taxid": 190310, "species_taxid": 190310, "relation_to_type": "type", "validated": true, "ani": 79.5658, "matched_fragments": 595, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella sediminis", "strain": "strain=HAW-EB3", "accession": "GCA_000018025.1", "taxid": 271097, "species_taxid": 271097, "relation_to_type": "type", "validated": true, "ani": 79.4934, "matched_fragments": 376, "total_fragments": 1640, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002836205.1", "gtdb_species": "s__Shewanella sp002836205", "ani": 94.6733, "matched_fragments": 1470, "total_fragments": 1640, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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"min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000019185.1", "gtdb_species": "s__Shewanella halifaxensis", "ani": 79.6131, "matched_fragments": 638, "total_fragments": 1640, "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_003966225.1", "gtdb_species": "s__Shewanella canadensis", "ani": 79.6118, "matched_fragments": 383, "total_fragments": 1640, "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", 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"gtdb_species": "s__Shewanella sp001957135", "ani": 78.2841, "matched_fragments": 277, "total_fragments": 1640, "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": -0.302, "cell_length": 0.0, "doubling_h": 0.214, "growth_tmp": 16.95, "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": 1.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.0, "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", "gelidimarina" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }