{ "type": "genome", "identifier": "GCF_003012345.1", "organism": "Phytohalomonas tamaricis", "title": "Phytohalomonas tamaricis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Chinese Academy of Forestry", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003012345.1", "bioproject": "PRJNA224116", "biosample": "SAMN08450111", "wgs_master": "PVRV00000000.1", "refseq_category": "reference genome", "taxid": "2081032", "species_taxid": "2081032", "organism_name": "Phytohalomonas tamaricis", "infraspecific_name": "strain=R4HLG17", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/03/20", "asm_name": "ASM301234v1", "asm_submitter": "Chinese Academy of Forestry", "gbrs_paired_asm": "GCA_003012345.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/012/345/GCF_003012345.1_ASM301234v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3623746", "genome_size_ungapped": "3623746", "gc_percent": "55.000000", "replicon_count": "0", "scaffold_count": "24", "contig_count": "24", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003012345.1-RS_2024_10_26", "annotation_date": "2024-10-26", "total_gene_count": "3366", "protein_coding_gene_count": "3266", "non_coding_gene_count": "73", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-03-20", "dateModified": "2018-03-20", "datePublished": "2018-03-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Phytohalomonas tamaricis" ], "sample_taxid": [ "2081032" ], "sample_host_organism": [ "Tamarix ramosissima" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Kumtag Desert, Xinjiang" ], "sample_host_location_id": [], "data_size": "1.032 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)": "3623746", "Number of Sequences": "24", "Longest Sequences (bp)": "962982", "N50 (bp)": "639256", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.1", "Number of CDSs": "3323", "Average Protein Length": "312.9", "Coding Ratio (%)": "86.1", "Number of rRNAs": "3", "Number of tRNAs": "63", "Number of CRISPRs": "1" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Salinicola peritrichatus", "strain": "strain=JCM 18795", "accession": "GCA_003206715.1", "taxid": 1267424, "species_taxid": 1267424, "relation_to_type": "type", "validated": true, "ani": 77.7881, "matched_fragments": 204, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lutea", "strain": "strain=KCTC 12847", "accession": "GCA_014651575.1", "taxid": 453962, "species_taxid": 453962, "relation_to_type": "type", "validated": true, "ani": 77.5876, "matched_fragments": 199, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas populi", "strain": "strain=MC", "accession": "GCA_003989825.1", "taxid": 2498858, "species_taxid": 2498858, "relation_to_type": "type", "validated": true, "ani": 77.499, "matched_fragments": 81, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria sinocarnis", "strain": "strain=DSM 23229", "accession": "GCA_003633775.1", "taxid": 595502, "species_taxid": 595502, "relation_to_type": "type", "validated": true, "ani": 77.4964, "matched_fragments": 201, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas lutea", "strain": "strain=DSM 23508", "accession": "GCA_000378505.1", "taxid": 453962, "species_taxid": 453962, "relation_to_type": "type", "validated": true, "ani": 77.4728, "matched_fragments": 194, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas organivorans", "strain": "strain=CECT 5995", "accession": "GCA_014192055.1", "taxid": 257772, "species_taxid": 257772, "relation_to_type": "type", "validated": true, "ani": 77.4547, "matched_fragments": 143, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas endophytica", "strain": "strain=MC28", "accession": "GCA_002879615.1", "taxid": 2033802, "species_taxid": 2033802, "relation_to_type": "type", "validated": true, "ani": 77.3412, "matched_fragments": 118, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas xinjiangensis", "strain": "strain=TRM 0175", "accession": "GCA_000759345.1", "taxid": 1166948, "species_taxid": 1166948, "relation_to_type": "type", "validated": true, "ani": 77.3384, "matched_fragments": 145, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas xianhensis", "strain": "strain=CGMCC 1.6848", "accession": "GCA_900113605.1", "taxid": 442341, "species_taxid": 442341, "relation_to_type": "type", "validated": true, "ani": 77.3345, "matched_fragments": 191, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas nanhaiensis", "strain": "strain=JCM 18142", "accession": "GCA_003990185.1", "taxid": 1258546, "species_taxid": 1258546, "relation_to_type": "type", "validated": true, "ani": 77.3297, "matched_fragments": 96, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Larsenimonas suaedae", "strain": "strain=DSM 22428", "accession": "GCA_023712105.1", "taxid": 1851019, "species_taxid": 1851019, "relation_to_type": "type", "validated": true, "ani": 77.3215, "matched_fragments": 150, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinicola endophyticus", "strain": "strain=CPA92", "accession": "GCA_003206575.1", "taxid": 1949083, "species_taxid": 1949083, "relation_to_type": "type", "validated": true, "ani": 77.2561, "matched_fragments": 201, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas zhangzhouensis", "strain": "strain=MCCC 1A11036", "accession": "GCA_021404465.1", "taxid": 2733481, "species_taxid": 2733481, "relation_to_type": "type", "validated": true, "ani": 77.2225, "matched_fragments": 123, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Salinicola halophyticus", "strain": "strain=CR45", "accession": "GCA_003206695.1", "taxid": 1808881, "species_taxid": 1808881, "relation_to_type": "type", "validated": true, "ani": 77.2092, "matched_fragments": 191, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Chromohalobacter nigrandesensis", "strain": "strain=DSM 14323", "accession": "GCA_023061285.1", "taxid": 119863, "species_taxid": 119863, "relation_to_type": "type", "validated": true, "ani": 77.2041, "matched_fragments": 159, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria indalinina", "strain": "strain=DSM 14324", "accession": "GCA_003385845.1", "taxid": 184067, "species_taxid": 184067, "relation_to_type": "type", "validated": true, "ani": 77.203, "matched_fragments": 198, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas sulfidivorans", "strain": "strain=MCCC 1A13718", "accession": "GCA_017868935.1", "taxid": 2733488, "species_taxid": 2733488, "relation_to_type": "type", "validated": true, "ani": 77.1789, "matched_fragments": 146, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria pakistanensis", "strain": "strain=KCTC 42082", "accession": "GCA_014652795.1", "taxid": 1508770, "species_taxid": 1508770, "relation_to_type": "type", "validated": true, "ani": 77.1788, "matched_fragments": 201, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas sulfidoxydans", "strain": "strain=MCCC 1A11059", "accession": "GCA_017868775.1", "taxid": 2733484, "species_taxid": 2733484, "relation_to_type": "type", "validated": true, "ani": 77.1514, "matched_fragments": 147, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas ethanolica", "strain": "strain=MCCC 1A11081", "accession": "GCA_021404305.1", "taxid": 2733486, "species_taxid": 2733486, "relation_to_type": "type", "validated": true, "ani": 77.1468, "matched_fragments": 145, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria konosiri", "strain": "strain=X49", "accession": "GCA_002155145.1", "taxid": 698828, "species_taxid": 698828, "relation_to_type": "type", "validated": true, "ani": 77.1373, "matched_fragments": 189, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas tianxiuensis", "strain": "strain=BC-M4-5", "accession": "GCA_009834345.1", "taxid": 2497861, "species_taxid": 2497861, "relation_to_type": "type", "validated": true, "ani": 77.0747, "matched_fragments": 156, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria phyllosphaerae", "strain": "strain=EAod3", "accession": "GCA_900312995.1", "taxid": 2100822, "species_taxid": 2100822, "relation_to_type": "type", "validated": true, "ani": 77.0221, "matched_fragments": 200, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Halomonas aerodenitrificans", "strain": "strain=MCCC 1A11058", "accession": "GCA_021404405.1", "taxid": 2733483, "species_taxid": 2733483, "relation_to_type": "type", "validated": true, "ani": 76.9008, "matched_fragments": 149, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria phosphatilytica", "strain": "strain=YCWA18", "accession": "GCA_001854625.1", "taxid": 657387, "species_taxid": 657387, "relation_to_type": "type", "validated": true, "ani": 76.7286, "matched_fragments": 168, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Kushneria phosphatilytica", "strain": "strain=YCWA18", "accession": "GCA_008247605.1", "taxid": 657387, "species_taxid": 657387, "relation_to_type": "type", "validated": true, "ani": 76.7178, "matched_fragments": 175, "total_fragments": 1200, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCA_003012345.1", "gtdb_species": "s__Phytohalomonas tamaricis", "ani": 100.0, "matched_fragments": 1199, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Phytohalomonas", "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_003206715.1", "gtdb_species": "s__Salinicola peritrichatus", "ani": 77.7881, "matched_fragments": 204, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola", "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_003990195.1", "gtdb_species": "s__Halomonas sp003990195", "ani": 77.6593, "matched_fragments": 81, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.00", "min_intra_species_ani": "98.34", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.91", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_000378505.1", "gtdb_species": "s__Halomonas_C lutea", "ani": 77.4436, "matched_fragments": 196, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001648175.1", "gtdb_species": "s__Halotalea alkalilenta_A", "ani": 77.4417, "matched_fragments": 153, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halotalea", "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_008274785.1", "gtdb_species": "s__Halomonas eurihalina", "ani": 77.3961, "matched_fragments": 136, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "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_900113605.1", "gtdb_species": "s__Halomonas_C xianhensis", "ani": 77.3648, "matched_fragments": 189, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.25", "min_intra_species_ani": "96.25", "mean_intra_species_af": "0.87", "min_intra_species_af": "0.87", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_000759345.1", "gtdb_species": "s__Halomonas_A xinjiangensis", "ani": 77.3384, "matched_fragments": 145, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_A", "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_000737985.1", "gtdb_species": "s__Salinicola sp000737985", "ani": 77.327, "matched_fragments": 191, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.18", "min_intra_species_ani": "96.18", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.88", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_001937195.1", "gtdb_species": "s__Salinicola socius", "ani": 77.3224, "matched_fragments": 179, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.48", "min_intra_species_ani": "98.96", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.93", "num_clustered_genomes": 3, "status": "-" }, { "accession": 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"s__Halomonas sp002119345", "ani": 77.2384, "matched_fragments": 97, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.32", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.86", "min_intra_species_af": "0.86", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014840935.1", "gtdb_species": "s__Halomonas_E sp014840935", "ani": 77.2256, "matched_fragments": 147, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E", "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_003385845.1", "gtdb_species": "s__Kushneria indalinina", "ani": 77.216, "matched_fragments": 197, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria", "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_014652795.1", "gtdb_species": "s__Kushneria pakistanensis", "ani": 77.1537, "matched_fragments": 203, "total_fragments": 1200, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria", "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_002155145.1", "gtdb_species": "s__Kushneria konosiri", "ani": 77.1511, "matched_fragments": 188, 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