{ "type": "genome", "identifier": "GCF_002777975.1", "organism": "Shewanella carassii", "title": "Shewanella carassii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "National Institute for Communicable Disease Control and Prevention, China CDC", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002777975.1", "bioproject": "PRJNA224116", "biosample": "SAMN07080850", "wgs_master": "NGVS00000000.1", "refseq_category": "na", "taxid": "1987584", "species_taxid": "1987584", "organism_name": "Shewanella carassii", "infraspecific_name": "strain=08MAS2251", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2017/11/16", "asm_name": "ASM277797v1", "asm_submitter": "National Institute for Communicable Disease Control and Prevention, China CDC", "gbrs_paired_asm": "GCA_002777975.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/777/975/GCF_002777975.1_ASM277797v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4375287", "genome_size_ungapped": "4375004", "gc_percent": "52.500000", "replicon_count": "0", "scaffold_count": "46", "contig_count": "46", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002777975.1-RS_2024_03_29", "annotation_date": "2024-03-29", "total_gene_count": "3986", "protein_coding_gene_count": "3810", "non_coding_gene_count": "120", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2017-11-16", "dateModified": "2017-11-16", "datePublished": "2017-11-16", "_annotation": { "sample_count": 1, "sample_organism": [ "Shewanella carassii" ], "sample_taxid": [ "1987584" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Maanshan" ], "sample_host_location_id": [], "data_size": "1.243 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)": "4375287", "Number of Sequences": "46", "Longest Sequences (bp)": "629576", "N50 (bp)": "301650", "Gap Ratio (%)": "0.007131", "GCcontent (%)": "52.7", "Number of CDSs": "3869", "Average Protein Length": "327.6", "Coding Ratio (%)": "86.9", "Number of rRNAs": "2", "Number of tRNAs": "110", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Shewanella carassii", "strain": "strain=08MAS2251", "accession": "GCA_002777975.1", "taxid": 1987584, "species_taxid": 1987584, 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"matched_fragments": 1320, "total_fragments": 1435, "ani_threshold": 95, "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": 93.8581, "matched_fragments": 1268, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella indica", "strain": "strain=KJW27", "accession": "GCA_002836975.1", "taxid": 768528, "species_taxid": 768528, "relation_to_type": "type", "validated": true, "ani": 93.832, "matched_fragments": 1221, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella indica", "strain": "strain=KCTC 23171", "accession": "GCA_014652115.1", "taxid": 768528, "species_taxid": 768528, "relation_to_type": "type", "validated": true, "ani": 93.7797, "matched_fragments": 1230, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=KCTC 22540", "accession": "GCA_014651975.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 93.5559, "matched_fragments": 1224, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=JC5", "accession": "GCA_003217175.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 93.5304, "matched_fragments": 1224, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella chilikensis", "strain": "strain=CCUG 57101", "accession": "GCA_023283475.1", "taxid": 558541, "species_taxid": 558541, "relation_to_type": "type", "validated": true, "ani": 93.5292, "matched_fragments": 1229, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": 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"accession": "GCA_023349185.1", "taxid": 260365, "species_taxid": 260365, "relation_to_type": "type", "validated": true, "ani": 78.3527, "matched_fragments": 383, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Shewanella insulae", "strain": "strain=JBTF-M18", "accession": "GCA_009831655.1", "taxid": 2681496, "species_taxid": 2681496, "relation_to_type": "type", "validated": true, "ani": 78.2463, "matched_fragments": 380, "total_fragments": 1435, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_002777975.1", "gtdb_species": "s__Shewanella carassii", "ani": 100.0, "matched_fragments": 1434, "total_fragments": 1435, "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_009183365.2", "gtdb_species": "s__Shewanella algae", "ani": 93.9015, "matched_fragments": 1316, "total_fragments": 1435, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.21", "min_intra_species_ani": "97.66", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 87, "status": "-" }, { "accession": "GCF_002836975.1", "gtdb_species": "s__Shewanella indica", "ani": 93.8331, "matched_fragments": 1221, "total_fragments": 1435, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella", "ani_circumscription_radius": 95.7827, "mean_intra_species_ani": "98.42", "min_intra_species_ani": 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"mean_intra_species_af": "0.93", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_003353085.1", "gtdb_species": "s__Shewanella corallii", "ani": 78.6998, "matched_fragments": 314, "total_fragments": 1435, "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_003957745.1", "gtdb_species": "s__Shewanella khirikhana", "ani": 78.6366, "matched_fragments": 462, "total_fragments": 1435, "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", "carassii" ], "quality": 3, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }