{ "type": "genome", "identifier": "GCF_900109735.1", "organism": "Atopomonas hussainii", "title": "Atopomonas hussainii", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900109735.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216214", "wgs_master": "FOAS00000000.1", "refseq_category": "reference genome", "taxid": "1429083", "species_taxid": "1429083", "organism_name": "Atopomonas hussainii", "infraspecific_name": "strain=JCM 19513", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/31", "asm_name": "IMG-taxon 2663763602 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900109735.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/109/735/GCF_900109735.1_IMG-taxon_2663763602_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": "3682314", "genome_size_ungapped": "3680748", "gc_percent": "59.000000", "replicon_count": "0", "scaffold_count": "45", "contig_count": "45", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900109735.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3521", "protein_coding_gene_count": "3431", "non_coding_gene_count": "70", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-31", "dateModified": "2016-10-31", "datePublished": "2016-10-31", "_annotation": { "sample_count": 1, "sample_organism": [ "Atopomonas hussainii" ], "sample_taxid": [ "1429083" ], "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": "1.033 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)": "3682314", "Number of Sequences": "45", "Longest Sequences (bp)": "359612", "N50 (bp)": "215245", "Gap Ratio (%)": "0.042528", "GCcontent (%)": "58.8", "Number of CDSs": "3449", "Average Protein Length": "323.6", "Coding Ratio (%)": "90.9", "Number of rRNAs": "7", "Number of tRNAs": "57", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Atopomonas hussainii", "strain": "strain=JCM 19513", "accession": "GCA_900109735.1", "taxid": 1429083, "species_taxid": 1429083, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1201, "total_fragments": 1203, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Pseudomonas sagittaria", "strain": "strain=JCM 18195", "accession": "GCA_900115715.1", "taxid": 1135990, "species_taxid": 1135990, "relation_to_type": "type", "validated": true, "ani": 78.6788, "matched_fragments": 370, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas aromaticivorans", "strain": "strain=MAP12", "accession": "GCA_019097855.1", "taxid": 2849492, "species_taxid": 2849492, "relation_to_type": "type", "validated": true, "ani": 78.6492, "matched_fragments": 343, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas linyingensis", "strain": "strain=LMG 25967", "accession": "GCA_900109175.1", "taxid": 915471, "species_taxid": 915471, "relation_to_type": "type", "validated": true, "ani": 78.6334, "matched_fragments": 351, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas insulae", "strain": "strain=UL073", "accession": "GCA_016901015.1", "taxid": 2809017, "species_taxid": 2809017, "relation_to_type": "type", "validated": true, "ani": 78.6199, "matched_fragments": 409, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas cavernae", "strain": "strain=K2W31S-8", "accession": "GCA_003595175.1", "taxid": 2320867, "species_taxid": 2320867, "relation_to_type": "type", "validated": true, "ani": 78.531, "matched_fragments": 420, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jinjuensis", "strain": "strain=NBRC 103047", "accession": "GCA_002091655.1", "taxid": 198616, "species_taxid": 198616, "relation_to_type": "type", "validated": true, "ani": 78.5274, 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"total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=RLD-1", "accession": "GCA_900187975.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 78.4427, "matched_fragments": 423, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas delhiensis", "strain": "strain=CCM 7361", "accession": "GCA_900099945.1", "taxid": 366289, "species_taxid": 366289, "relation_to_type": "type", "validated": true, "ani": 78.4081, "matched_fragments": 422, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas nitroreducens", "strain": "strain=NBRC 12694", "accession": "GCA_002091755.1", "taxid": 46680, "species_taxid": 46680, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3898, "matched_fragments": 377, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas nitroreducens", "strain": "strain=DSM 14399", "accession": "GCA_012986245.1", "taxid": 46680, "species_taxid": 46680, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3764, "matched_fragments": 390, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas mangrovi", "strain": "strain=TC11", "accession": "GCA_003052585.1", "taxid": 2161748, "species_taxid": 2161748, "relation_to_type": "type", "validated": true, "ani": 78.3467, "matched_fragments": 352, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas lalucatii", "strain": "strain=R1b54", "accession": "GCA_018398425.1", "taxid": 1424203, "species_taxid": 1424203, "relation_to_type": "type", "validated": true, "ani": 78.3303, "matched_fragments": 407, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas fakonensis", "strain": "strain=COW40", "accession": "GCA_019139895.1", "taxid": 2842355, "species_taxid": 2842355, "relation_to_type": "type", "validated": true, "ani": 78.3144, "matched_fragments": 352, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_900114065.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 78.1348, "matched_fragments": 313, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas kunmingensis", "strain": "strain=DSM 25974", "accession": "GCA_024397575.1", "taxid": 1211807, "species_taxid": 1211807, "relation_to_type": "type", "validated": true, "ani": 78.0981, "matched_fragments": 318, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas kribbensis", "strain": "strain=46-2", "accession": "GCA_003352185.1", "taxid": 1628086, "species_taxid": 1628086, "relation_to_type": "type", "validated": true, "ani": 78.0069, "matched_fragments": 324, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas vranovensis", "strain": "strain=DSM 16006", "accession": "GCA_000425805.1", "taxid": 321661, "species_taxid": 321661, "relation_to_type": "type", "validated": true, "ani": 77.8772, "matched_fragments": 299, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas aestusnigri", "strain": "strain=CECT 8317", "accession": "GCA_900108005.1", "taxid": 857252, "species_taxid": 857252, "relation_to_type": "type", "validated": true, "ani": 77.8695, "matched_fragments": 234, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas pisciculturae", "strain": "strain=P115", "accession": "GCA_015461805.1", 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"validated": true, "ani": 77.8205, "matched_fragments": 319, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas aestusnigri", "strain": "strain=VGXO14", "accession": "GCA_002197985.1", "taxid": 857252, "species_taxid": 857252, "relation_to_type": "type", "validated": true, "ani": 77.8089, "matched_fragments": 237, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas pachastrellae", "strain": "strain=JCM 12285", "accession": "GCA_900114765.1", "taxid": 254161, "species_taxid": 254161, "relation_to_type": "type", "validated": true, "ani": 77.73, "matched_fragments": 278, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas pachastrellae", "strain": "strain=CCUG 46540", "accession": "GCA_001989375.1", "taxid": 254161, "species_taxid": 254161, "relation_to_type": "type", "validated": true, "ani": 77.709, "matched_fragments": 272, "total_fragments": 1203, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900109735.1", "gtdb_species": "s__Pseudomonas_L hussainii", "ani": 100.0, "matched_fragments": 1201, "total_fragments": 1203, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_L", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "95.93", "min_intra_species_ani": "95.93", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_001592875.1", "gtdb_species": "s__Pseudomonas_E sp001592875", "ani": 78.9802, "matched_fragments": 401, "total_fragments": 1203, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E", 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95.0, "mean_intra_species_ani": "96.53", "min_intra_species_ani": "96.12", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.90", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_016919445.1", "gtdb_species": "s__Pseudomonas sp016919445", "ani": 78.3575, "matched_fragments": 394, "total_fragments": 1203, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas", "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_001708505.1", "gtdb_species": "s__Pseudomonas_F sp001708505", "ani": 78.347, "matched_fragments": 374, "total_fragments": 1203, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F", "ani_circumscription_radius": 95.0, 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