{ "type": "genome", "identifier": "GCF_900115045.1", "organism": "Izhakiella capsodis", "title": "Izhakiella capsodis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900115045.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216516", "wgs_master": "FOVC00000000.1", "refseq_category": "reference genome", "taxid": "1367852", "species_taxid": "1367852", "organism_name": "Izhakiella capsodis", "infraspecific_name": "strain=N6PO6", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/11/02", "asm_name": "IMG-taxon 2651870110 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900115045.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/115/045/GCF_900115045.1_IMG-taxon_2651870110_annotated_assembly", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3508271", "genome_size_ungapped": "3507996", "gc_percent": "50.000000", "replicon_count": "0", "scaffold_count": "30", "contig_count": "30", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900115045.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3279", "protein_coding_gene_count": "3063", "non_coding_gene_count": "71", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-11-02", "dateModified": "2016-11-02", "datePublished": "2016-11-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Izhakiella capsodis" ], "sample_taxid": [ "1367852" ], "sample_host_organism": [ "not applicable" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "missing" ], "sample_host_location_id": [], "data_size": "1.002 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)": "3508271", "Number of Sequences": "30", "Longest Sequences (bp)": "750464", "N50 (bp)": "296782", "Gap Ratio (%)": "0.007839", "GCcontent (%)": "50.1", "Number of CDSs": "3204", "Average Protein Length": "302.2", "Coding Ratio (%)": "82.8", "Number of rRNAs": "5", "Number of tRNAs": "58", "Number of CRISPRs": "3" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Izhakiella capsodis", "strain": "strain=N6PO6", "accession": "GCA_900115045.1", "taxid": 1367852, "species_taxid": 1367852, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1155, "total_fragments": 1155, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Izhakiella australiensis", "strain": "strain=D4N98", "accession": "GCA_002006995.1", "taxid": 1926881, "species_taxid": 1926881, "relation_to_type": "type", "validated": true, "ani": 82.7331, "matched_fragments": 843, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "[Pantoea] beijingensis", "strain": "strain=JZB2120001", "accession": "GCA_022647505.1", "taxid": 1324864, "species_taxid": 1324864, "relation_to_type": "type", "validated": true, "ani": 78.3672, "matched_fragments": 255, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia iniecta", "strain": "strain=B120", "accession": "GCA_001267535.1", "taxid": 1560201, "species_taxid": 1560201, "relation_to_type": "type", 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"organism_name": "Mixta tenebrionis", "strain": "strain=BIT-26", "accession": "GCA_006517625.1", "taxid": 2562439, "species_taxid": 2562439, "relation_to_type": "type", "validated": true, "ani": 77.7979, "matched_fragments": 322, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter muytjensii", "strain": "strain=ATCC 51329", "accession": "GCA_001277195.1", "taxid": 413501, "species_taxid": 413501, "relation_to_type": "type", "validated": true, "ani": 77.7593, "matched_fragments": 218, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia aphidicola", "strain": "strain=JCM 21238", "accession": "GCA_014773485.1", "taxid": 68334, "species_taxid": 68334, "relation_to_type": "type", "validated": true, "ani": 77.7577, "matched_fragments": 318, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Siccibacter turicensis", "strain": "strain=LMG 23730", "accession": "GCA_000463155.2", "taxid": 357233, "species_taxid": 357233, "relation_to_type": "type", "validated": true, "ani": 77.7079, "matched_fragments": 206, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Erwinia pyrifoliae", "strain": "strain=DSM 12163", "accession": "GCA_000026985.1", "taxid": 79967, "species_taxid": 79967, "relation_to_type": "type", "validated": true, "ani": 77.7043, "matched_fragments": 270, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pantoea rwandensis", "strain": "strain=LMG 26275", "accession": "GCA_002095475.1", "taxid": 1076550, "species_taxid": 1076550, "relation_to_type": "type", "validated": true, "ani": 77.6774, "matched_fragments": 248, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter muytjensii", "strain": "strain=ATCC 51329", "accession": "GCA_000409285.1", "taxid": 413501, "species_taxid": 413501, "relation_to_type": "type", "validated": true, "ani": 77.6749, "matched_fragments": 216, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus cabanillasii", "strain": "strain=DSM 17905", "accession": "GCA_003386665.1", "taxid": 351673, "species_taxid": 351673, "relation_to_type": "type", "validated": true, "ani": 77.5715, "matched_fragments": 89, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Xenorhabdus vietnamensis", "strain": "strain=DSM 22392", "accession": "GCA_002127535.1", "taxid": 351656, "species_taxid": 351656, "relation_to_type": "type", "validated": true, "ani": 77.5501, "matched_fragments": 83, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter dublinensis subsp. lactaridi", "strain": "strain=LMG 23825", "accession": "GCA_000409345.1", "taxid": 413499, "species_taxid": 413497, 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"matched_fragments": 172, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Cronobacter sakazakii", "strain": "strain=ATCC 29544", "accession": "GCA_001971035.1", "taxid": 28141, "species_taxid": 28141, "relation_to_type": "type", "validated": true, "ani": 77.1546, "matched_fragments": 206, "total_fragments": 1155, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900115045.1", "gtdb_species": "s__Izhakiella capsodis", "ani": 100.0, "matched_fragments": 1155, "total_fragments": 1155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Izhakiella", "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": 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persicina_A", "ani": 78.0655, "matched_fragments": 264, "total_fragments": 1155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "99.46", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.97", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_019132875.1", "gtdb_species": "s__Erwinia sp019132875", "ani": 78.0085, "matched_fragments": 304, "total_fragments": 1155, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Erwinia", "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_003751505.1", "gtdb_species": "s__Erwinia sp003751505", "ani": 77.9903, 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