{ "type": "genome", "identifier": "GCF_900105255.1", "organism": "Halopseudomonas sabulinigri", "title": "Halopseudomonas sabulinigri", "description": "na", "data type": "Genome sequencing and assembly", "organization": "DOE - JOINT GENOME INSTITUTE", "publication": [ {} ], "properties": { "assembly_accession": "GCF_900105255.1", "bioproject": "PRJNA224116", "biosample": "SAMN05216271", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "472181", "species_taxid": "472181", "organism_name": "Halopseudomonas sabulinigri", "infraspecific_name": "strain=JCM 14963", "isolate": "na", "version_status": "latest", "assembly_level": "Chromosome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2016/10/21", "asm_name": "IMG-taxon 2675902958 annotated assembly", "asm_submitter": "DOE - JOINT GENOME INSTITUTE", "gbrs_paired_asm": "GCA_900105255.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/900/105/255/GCF_900105255.1_IMG-taxon_2675902958_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": "4030203", "genome_size_ungapped": "4030103", "gc_percent": "60.000000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_900105255.1-RS_2024_12_11", "annotation_date": "2024-12-11", "total_gene_count": "3706", "protein_coding_gene_count": "3615", "non_coding_gene_count": "64", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2016-10-21", "dateModified": "2016-10-21", "datePublished": "2016-10-21", "_annotation": { "sample_count": 1, "sample_organism": [ "Halopseudomonas sabulinigri" ], "sample_taxid": [ "472181" ], "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": "1.131 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)": "4030103", "Number of Sequences": "1", "Longest Sequences (bp)": "4030103", "N50 (bp)": "4030103", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "59.9", "Number of CDSs": "3680", "Average Protein Length": "330.3", "Coding Ratio (%)": "90.5", "Number of rRNAs": "9", "Number of tRNAs": "53", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Halopseudomonas pachastrellae", "strain": "strain=JCM 12285", "accession": "GCA_900114765.1", "taxid": 254161, "species_taxid": 254161, "relation_to_type": "type", "validated": true, "ani": 81.2587, "matched_fragments": 744, "total_fragments": 1343, "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": 81.2126, "matched_fragments": 740, "total_fragments": 1343, "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": 80.9109, "matched_fragments": 699, "total_fragments": 1343, "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": 80.8613, "matched_fragments": 713, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas oceani", "strain": "strain=CGMCC 1.15195", "accession": "GCA_014641295.1", "taxid": 1708783, "species_taxid": 1708783, "relation_to_type": "type", "validated": true, "ani": 80.8159, "matched_fragments": 684, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas oceani", "strain": "strain=DSM 100277", "accession": "GCA_002903165.1", "taxid": 1708783, "species_taxid": 1708783, "relation_to_type": "type", "validated": true, "ani": 80.8031, "matched_fragments": 670, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas litoralis", "strain": "strain=2SM5", "accession": "GCA_900105005.1", "taxid": 797277, "species_taxid": 797277, "relation_to_type": "type", "validated": true, "ani": 79.1221, "matched_fragments": 410, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas bauzanensis", "strain": "strain=CGMCC 1.9095", "accession": "GCA_900114735.1", "taxid": 653930, "species_taxid": 653930, "relation_to_type": "type", "validated": true, "ani": 79.0413, "matched_fragments": 421, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas bauzanensis", "strain": "strain=DSM 22558", "accession": "GCA_900111225.1", "taxid": 653930, "species_taxid": 653930, "relation_to_type": "type", "validated": true, "ani": 79.0014, "matched_fragments": 426, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas salina", "strain": "strain=CGMCC 1.12482", "accession": "GCA_014637955.1", "taxid": 1323744, "species_taxid": 1323744, "relation_to_type": "type", "validated": true, "ani": 78.5873, "matched_fragments": 407, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halopseudomonas salina", "strain": "strain=XCD-X85", "accession": "GCA_008641105.1", "taxid": 1323744, "species_taxid": 1323744, "relation_to_type": "type", "validated": true, "ani": 78.5829, "matched_fragments": 402, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas saliphila", "strain": "strain=16W4-4-3", "accession": "GCA_008638345.1", "taxid": 2586906, "species_taxid": 2586906, "relation_to_type": "type", "validated": true, "ani": 78.5441, "matched_fragments": 403, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas hydrolytica", "strain": "strain=DSWY01", "accession": "GCA_021495345.2", "taxid": 2493633, "species_taxid": 2493633, "relation_to_type": "type", "validated": true, "ani": 78.417, "matched_fragments": 407, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=FDAARGOS_876", "accession": "GCA_016028635.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "suspected-type", "validated": true, "ani": 78.3545, "matched_fragments": 320, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas yangonensis", "strain": "strain=MY50", "accession": "GCA_009932725.1", "taxid": 2579922, "species_taxid": 2579922, "relation_to_type": "type", "validated": true, "ani": 78.154, "matched_fragments": 330, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas eucalypticola", "strain": "strain=NP-1", "accession": "GCA_013374995.1", "taxid": 2599595, "species_taxid": 2599595, "relation_to_type": "type", "validated": true, "ani": 78.0733, "matched_fragments": 268, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=DSM 50238", "accession": "GCA_002891015.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "type", "validated": true, "ani": 78.0721, "matched_fragments": 313, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas degradans", "strain": "strain=DSM 50238", "accession": "GCA_024448505.1", "taxid": 2968968, "species_taxid": 2968968, "relation_to_type": "type", "validated": true, "ani": 78.0536, "matched_fragments": 308, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas chlororaphis subsp. aurantiaca", "strain": "strain=DSM 19603", "accession": "GCA_003851835.1", "taxid": 86192, "species_taxid": 587753, "relation_to_type": "type", "validated": true, "ani": 78.0333, "matched_fragments": 318, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas japonica", "strain": "strain=NBRC 103040", "accession": "GCA_000730585.1", "taxid": 256466, "species_taxid": 256466, "relation_to_type": "type", "validated": true, "ani": 77.9328, "matched_fragments": 318, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas japonica", "strain": "strain=DSM 22348", "accession": "GCA_900188455.1", "taxid": 256466, "species_taxid": 256466, "relation_to_type": "type", "validated": true, "ani": 77.8149, "matched_fragments": 317, "total_fragments": 1343, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_900105255.1", "gtdb_species": "s__Pseudomonas_D sabulinigri", "ani": 100.0, "matched_fragments": 1342, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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": "conclusive" }, { "accession": "GCF_003797905.1", "gtdb_species": "s__Pseudomonas_D sp002683975", "ani": 81.6006, "matched_fragments": 816, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.94", "min_intra_species_ani": "98.05", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.90", "num_clustered_genomes": 5, "status": "-" }, { "accession": "GCA_011053055.1", "gtdb_species": "s__Pseudomonas_D sabulinigri_A", "ani": 81.4171, "matched_fragments": 829, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.96", "min_intra_species_ani": "99.96", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.96", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_900114765.1", "gtdb_species": "s__Pseudomonas_D pachastrellae", "ani": 81.2569, "matched_fragments": 743, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.15", "min_intra_species_ani": "95.72", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.72", "num_clustered_genomes": 17, "status": "-" }, { "accession": "GCF_002197985.1", "gtdb_species": "s__Pseudomonas_D aestusnigri", "ani": 80.9111, "matched_fragments": 699, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.11", "min_intra_species_ani": "96.74", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.81", "num_clustered_genomes": 25, "status": "-" }, { "accession": "GCF_003444685.1", "gtdb_species": "s__Pseudomonas_D gallaeciensis", "ani": 80.8999, "matched_fragments": 771, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.87", "min_intra_species_ani": "97.82", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_002903165.1", "gtdb_species": "s__Pseudomonas_D oceani", "ani": 80.8026, "matched_fragments": 669, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCA_002296055.1", "gtdb_species": "s__Pseudomonas_D sp002296055", "ani": 80.3224, "matched_fragments": 595, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_000939975.1", "gtdb_species": "s__Pseudomonas_D saudimassiliensis", "ani": 79.3791, "matched_fragments": 451, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_009497895.1", "gtdb_species": "s__Pseudomonas_D pelagia_A", "ani": 79.2053, "matched_fragments": 496, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_008365385.1", "gtdb_species": "s__Pseudomonas_D laoshanensis", "ani": 79.1585, "matched_fragments": 456, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.00", "min_intra_species_ani": "95.95", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002979975.1", "gtdb_species": "s__Pseudomonas_D sp002979975", "ani": 79.1324, "matched_fragments": 479, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_000410875.1", "gtdb_species": "s__Pseudomonas_D pelagia", "ani": 79.0644, "matched_fragments": 446, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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_900114735.1", "gtdb_species": "s__Pseudomonas_D bauzanensis", "ani": 79.0205, "matched_fragments": 423, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.15", "min_intra_species_ani": "98.30", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_900114825.1", "gtdb_species": "s__Pseudomonas_D yangmingensis", "ani": 78.9612, "matched_fragments": 390, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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": "GCA_019116555.1", "gtdb_species": "s__Pseudomonas_D excrementavium", "ani": 78.7946, "matched_fragments": 354, "total_fragments": 1343, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D", "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": null, "cell_length": null, "doubling_h": null, "growth_tmp": null, "optimum_tmp": null, "optimum_ph": null, "genome_size": null, "gc_content": null, "coding_genes": null, "rRNA16S_genes": null, "tRNA_genes": null, "gram_stain": null, "sporulation": null, "motility": null, "range_salinity": null, "facultative_respiration": null, "anaerobic_respiration": null, "aerobic_respiration": null, "mesophilic_range_tmp": null, "thermophilic_range_tmp": null, "psychrophilic_range_tmp": null, "bacillus_cell_shape": null, "coccus_cell_shape": null, "filament_cell_shape": null, "coccobacillus_cell_shape": null, "vibrio_cell_shape": null, "spiral_cell_shape": null }, "_genome_taxon": [ "Halopseudomonas", "sabulinigri" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }