{ "type": "genome", "identifier": "GCF_000164865.1", "organism": "[Enterobacter] lignolyticus SCF1", "title": "[Enterobacter] lignolyticus SCF1", "description": "na", "data type": "Genome sequencing and assembly", "organization": "US DOE Joint Genome Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000164865.1", "bioproject": "PRJNA224116", "biosample": "SAMN00116754", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "701347", "species_taxid": "1334193", "organism_name": "[Enterobacter] lignolyticus SCF1", "infraspecific_name": "strain=SCF1", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2010/10/15", "asm_name": "ASM16486v1", "asm_submitter": "US DOE Joint Genome Institute", "gbrs_paired_asm": "GCA_000164865.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/164/865/GCF_000164865.1_ASM16486v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4814049", "genome_size_ungapped": "4814049", "gc_percent": "57.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000164865.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4554", "protein_coding_gene_count": "4404", "non_coding_gene_count": "111", "pubmed_id": "22180812" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2010-10-15", "dateModified": "2010-10-15", "datePublished": "2010-10-15", "_annotation": { "sample_count": 1, "sample_organism": [ "[Enterobacter] lignolyticus SCF1" ], "sample_taxid": [ "701347" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "USA: Luquillo LTER, Puerto Rico" ], "sample_host_location_id": [], "data_size": "1.355 MB", "sample_ph_range": { "min": 5575.0, "max": 5575.0 }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4814049", "Number of Sequences": "1", "Longest Sequences (bp)": "4814049", "N50 (bp)": "4814049", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "57.0", "Number of CDSs": "4443", "Average Protein Length": "320.2", "Coding Ratio (%)": "88.7", "Number of rRNAs": "22", "Number of tRNAs": "82", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Klebsiella quasipneumoniae", "strain": "strain=FDAARGOS_1503", "accession": "GCA_020099175.1", "taxid": 1463165, "species_taxid": 1463165, "relation_to_type": "type", "validated": true, "ani": 82.8802, "matched_fragments": 1000, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella quasipneumoniae subsp. quasipneumoniae", "strain": "strain=01A030T", "accession": "GCA_020525925.1", "taxid": 1667327, "species_taxid": 1463165, "relation_to_type": "type", "validated": true, "ani": 82.8601, "matched_fragments": 994, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=FDAARGOS 1430", "accession": "GCA_019047025.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 82.8265, "matched_fragments": 954, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_001729805.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 82.8069, "matched_fragments": 953, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter chengduensis", "strain": "strain=WCHECl-C4 = WCHECh050004", "accession": "GCA_001984825.2", "taxid": 2494701, "species_taxid": 2494701, "relation_to_type": "type", "validated": true, "ani": 82.7766, "matched_fragments": 973, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 82.7348, "matched_fragments": 958, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella quasipneumoniae", "strain": "strain=DSM 28211", "accession": "GCA_020115515.1", "taxid": 1463165, "species_taxid": 1463165, "relation_to_type": "type", "validated": true, "ani": 82.6844, "matched_fragments": 987, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella quasivariicola", "strain": "strain=KPN1705", "accession": "GCA_002269255.1", "taxid": 2026240, "species_taxid": 2026240, "relation_to_type": "type", "validated": true, "ani": 82.6487, "matched_fragments": 975, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 82.647, "matched_fragments": 933, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yokenella regensburgei", "strain": "strain=NCTC11966", "accession": "GCA_900460805.1", "taxid": 158877, "species_taxid": 158877, "relation_to_type": "type", "validated": true, "ani": 82.6258, "matched_fragments": 1038, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. oharae", "strain": "strain=DSM 16687", "accession": "GCA_001729705.1", "taxid": 301102, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 82.6196, "matched_fragments": 948, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. oharae", "strain": "strain=FDAARGOS_1533", "accession": "GCA_020097195.1", "taxid": 301102, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 82.5998, "matched_fragments": 933, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Raoultella terrigena", "strain": "strain=NBRC 14941", "accession": "GCA_006539725.1", "taxid": 577, "species_taxid": 577, "relation_to_type": "type", "validated": true, "ani": 82.5692, "matched_fragments": 997, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella pneumoniae subsp. pneumoniae", "strain": "strain=ATCC 13883", "accession": "GCA_000788015.1", "taxid": 72407, "species_taxid": 573, "relation_to_type": "type", "validated": true, "ani": 82.5433, "matched_fragments": 974, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kluyvera georgiana", "strain": "strain=ATCC 51603", "accession": "GCA_001654985.1", "taxid": 73098, "species_taxid": 73098, "relation_to_type": "type", "validated": true, "ani": 82.5017, "matched_fragments": 910, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella michiganensis", "strain": "strain=DSM 25444", "accession": "GCA_002925905.1", "taxid": 1134687, "species_taxid": 1134687, "relation_to_type": "type", "validated": true, "ani": 82.4977, "matched_fragments": 988, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. xiangfangensis", "strain": "strain=LMG27195", "accession": "GCA_001729785.1", "taxid": 1296536, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 82.4418, "matched_fragments": 927, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Yokenella regensburgei", "strain": "strain=ATCC 49455", "accession": "GCA_000735455.1", "taxid": 158877, "species_taxid": 158877, "relation_to_type": "type", "validated": true, "ani": 82.4211, "matched_fragments": 1011, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella grimontii", "strain": "strain=06D021", "accession": "GCA_900200035.1", "taxid": 2058152, "species_taxid": 2058152, "relation_to_type": "type", "validated": true, "ani": 82.4143, "matched_fragments": 991, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 82.3013, "matched_fragments": 918, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_021278985.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 82.2775, "matched_fragments": 940, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=NBRC 105723", "accession": "GCA_000759815.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 82.2194, "matched_fragments": 909, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella oxytoca", "strain": "strain=NCTC13727", "accession": "GCA_900636985.1", "taxid": 571, "species_taxid": 571, "relation_to_type": "type", "validated": true, "ani": 82.1804, "matched_fragments": 970, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=DSM 16636", "accession": "GCA_015965555.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 82.1662, "matched_fragments": 904, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Citrobacter rodentium", "strain": "strain=ATCC 51116", "accession": "GCA_015965415.1", "taxid": 67825, "species_taxid": 67825, "relation_to_type": "type", "validated": true, "ani": 82.1473, "matched_fragments": 910, "total_fragments": 1604, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Klebsiella oxytoca", "strain": "strain=NBRC 105695", "accession": "GCA_001598695.1", "taxid": 571, "species_taxid": 571, 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"num_clustered_genomes": 644, "status": "-" }, { "accession": "GCF_900322725.1", "gtdb_species": "s__Enterobacter quasihormaechei", "ani": 82.6242, "matched_fragments": 931, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_003594915.1", "gtdb_species": "s__Enterobacter chuandaensis", "ani": 82.6204, "matched_fragments": 952, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", 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"status": "-" }, { "accession": "GCF_002925905.1", "gtdb_species": "s__Klebsiella michiganensis", "ani": 82.4904, "matched_fragments": 991, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.53", "min_intra_species_ani": "97.41", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 291, "status": "-" }, { "accession": "GCF_003634515.1", "gtdb_species": "s__Enterobacter asburiae_A", "ani": 82.486, "matched_fragments": 991, "total_fragments": 1604, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.0274, "mean_intra_species_ani": "97.62", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": 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