{ "type": "genome", "identifier": "GCF_004681125.1", "organism": "Polymorphobacter arshaanensis", "title": "Polymorphobacter arshaanensis", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Institute of Microbiology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_004681125.1", "bioproject": "PRJNA224116", "biosample": "SAMN10829600", "wgs_master": "SIHO00000000.1", "refseq_category": "reference genome", "taxid": "2511025", "species_taxid": "2511025", "organism_name": "Polymorphobacter arshaanensis", "infraspecific_name": "strain=DJ1R-1", "isolate": "na", "version_status": "latest", "assembly_level": "Scaffold", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/04/02", "asm_name": "ASM468112v1", "asm_submitter": "Institute of Microbiology", "gbrs_paired_asm": "GCA_004681125.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/004/681/125/GCF_004681125.1_ASM468112v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "3257822", "genome_size_ungapped": "3257735", "gc_percent": "65.000000", "replicon_count": "0", "scaffold_count": "10", "contig_count": "10", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_004681125.1-RS_2024_04_16", "annotation_date": "2024-04-16", "total_gene_count": "3136", "protein_coding_gene_count": "3066", "non_coding_gene_count": "54", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-04-02", "dateModified": "2019-04-02", "datePublished": "2019-04-02", "_annotation": { "sample_count": 1, "sample_organism": [ "Polymorphobacter arshaanensis" ], "sample_taxid": [ "2511025" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China:Dujuan lake" ], "sample_host_location_id": [], "data_size": "0.890 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)": "3257822", "Number of Sequences": "10", "Longest Sequences (bp)": "1330964", "N50 (bp)": "1178364", "Gap Ratio (%)": "0.002824", "GCcontent (%)": "65.0", "Number of CDSs": "3080", "Average Protein Length": "319.8", "Coding Ratio (%)": "90.7", "Number of rRNAs": "3", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Polymorphobacter fuscus", "strain": "strain=D40P", "accession": "GCA_009607675.1", "taxid": 1439888, "species_taxid": 1439888, "relation_to_type": "type", "validated": true, "ani": 78.8893, "matched_fragments": 418, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polymorphobacter fuscus", "strain": "strain=D40P", "accession": "GCA_009372075.1", "taxid": 1439888, "species_taxid": 1439888, "relation_to_type": "type", "validated": true, "ani": 78.879, "matched_fragments": 419, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polymorphobacter fuscus", "strain": "strain=DSM 105347", "accession": "GCA_011927825.1", "taxid": 1439888, "species_taxid": 1439888, "relation_to_type": "type", "validated": true, "ani": 78.7957, "matched_fragments": 416, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polymorphobacter glacialis", "strain": "strain=CGMCC 1.15519", "accession": "GCA_014643455.1", "taxid": 1614636, "species_taxid": 1614636, "relation_to_type": "type", "validated": true, "ani": 78.5799, "matched_fragments": 366, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polymorphobacter multimanifer", "strain": "strain=DSM 102189", "accession": "GCA_014205635.1", "taxid": 1070431, "species_taxid": 1070431, "relation_to_type": "type", "validated": true, "ani": 78.1203, "matched_fragments": 312, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Polymorphobacter multimanifer", "strain": "strain=JCM 18140", "accession": "GCA_014647295.1", "taxid": 1070431, "species_taxid": 1070431, "relation_to_type": "type", "validated": true, "ani": 78.1102, "matched_fragments": 286, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sandarakinorhabdus oryzae", "strain": "strain=NM-18", "accession": "GCA_009733735.1", "taxid": 2675220, "species_taxid": 2675220, "relation_to_type": "type", "validated": true, "ani": 78.0862, "matched_fragments": 286, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sandarakinorhabdus rubra", "strain": "strain=MO-4", "accession": "GCA_010994245.1", "taxid": 2672568, "species_taxid": 2672568, "relation_to_type": "type", "validated": true, "ani": 77.9605, "matched_fragments": 252, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas ginsenosidivorax", "strain": "strain=KHI67", "accession": "GCA_007995065.1", "taxid": 862135, "species_taxid": 862135, "relation_to_type": "type", "validated": true, "ani": 77.7807, "matched_fragments": 285, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingosinicella soli", "strain": "strain=DSM 17328", "accession": "GCA_014199685.1", "taxid": 333708, "species_taxid": 333708, "relation_to_type": "type", "validated": true, "ani": 77.7422, "matched_fragments": 272, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hengshuiensis", "strain": "strain=WHSC-8", "accession": "GCA_000935025.1", "taxid": 1609977, "species_taxid": 1609977, "relation_to_type": "type", "validated": true, "ani": 77.7346, "matched_fragments": 264, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas populi", "strain": "strain=3-7", "accession": "GCA_004208535.1", "taxid": 2484750, "species_taxid": 2484750, "relation_to_type": "type", "validated": true, "ani": 77.5732, "matched_fragments": 270, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas endophytica", "strain": "strain=DSM 101535", "accession": "GCA_014199415.1", "taxid": 869719, "species_taxid": 869719, "relation_to_type": "type", "validated": true, "ani": 77.5689, "matched_fragments": 240, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingosinicella microcystinivorans", "strain": "strain=DSM 19791", "accession": "GCA_003634215.1", "taxid": 335406, "species_taxid": 335406, "relation_to_type": "type", "validated": true, "ani": 77.5339, "matched_fragments": 244, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis indica", "strain": "strain=DS15", "accession": "GCA_900188185.1", "taxid": 436663, "species_taxid": 436663, "relation_to_type": "type", "validated": true, "ani": 77.527, "matched_fragments": 256, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis solisilvae", "strain": "strain=R366", "accession": "GCA_015475875.1", "taxid": 1886788, "species_taxid": 1886788, "relation_to_type": "type", "validated": true, "ani": 77.5145, "matched_fragments": 231, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas rhizophila", "strain": "strain=KACC 19189", "accession": "GCA_014396585.1", "taxid": 2071607, "species_taxid": 2071607, "relation_to_type": "type", "validated": true, "ani": 77.469, "matched_fragments": 181, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas flavalba", "strain": "strain=ZLT-5", "accession": "GCA_004796535.1", "taxid": 2559804, "species_taxid": 2559804, "relation_to_type": "type", "validated": true, "ani": 77.4376, "matched_fragments": 259, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas oleivorans", "strain": "strain=FW-11", "accession": "GCA_003050615.1", "taxid": 1735121, "species_taxid": 1735121, "relation_to_type": "type", "validated": true, "ani": 77.3721, "matched_fragments": 203, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis fribergensis", "strain": "strain=Kp5.2", "accession": "GCA_000803645.1", "taxid": 1515612, "species_taxid": 1515612, "relation_to_type": "type", "validated": true, "ani": 77.358, "matched_fragments": 249, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas citri", "strain": "strain=RRHST34", "accession": "GCA_019429485.1", "taxid": 2862499, "species_taxid": 2862499, "relation_to_type": "type", "validated": true, "ani": 77.3416, "matched_fragments": 254, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis alaskensis", "strain": "strain=RB2256", "accession": "GCA_000013985.1", "taxid": 117207, "species_taxid": 117207, "relation_to_type": "type", "validated": true, "ani": 77.3332, "matched_fragments": 248, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis bauzanensis", "strain": "strain=CGMCC 1.8959", "accession": "GCA_014645635.1", "taxid": 651663, "species_taxid": 651663, "relation_to_type": "type", "validated": true, "ani": 77.3087, "matched_fragments": 221, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingopyxis bauzanensis", "strain": "strain=DSM 22271", "accession": "GCA_002205675.1", "taxid": 651663, "species_taxid": 651663, "relation_to_type": "type", "validated": true, "ani": 77.3063, "matched_fragments": 224, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas yunnanensis", "strain": "strain=YIM 3", "accession": "GCA_019898765.1", "taxid": 310400, "species_taxid": 310400, "relation_to_type": "type", "validated": true, "ani": 77.2337, "matched_fragments": 246, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas jatrophae", "strain": "strain=S5-249", "accession": "GCA_900113315.1", "taxid": 1166337, "species_taxid": 1166337, "relation_to_type": "type", "validated": true, "ani": 77.2064, "matched_fragments": 234, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas folli", "strain": "strain=RHCKR7", "accession": "GCA_019429525.1", "taxid": 2862497, "species_taxid": 2862497, "relation_to_type": "type", "validated": true, "ani": 77.106, "matched_fragments": 271, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas profundi", "strain": "strain=LMO-1", "accession": "GCA_009739515.1", "taxid": 2681549, "species_taxid": 2681549, "relation_to_type": "type", "validated": true, "ani": 76.9536, "matched_fragments": 247, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas morindae", "strain": "strain=NBD5", "accession": "GCA_023822065.1", "taxid": 1541170, "species_taxid": 1541170, "relation_to_type": "type", "validated": true, "ani": 76.9203, "matched_fragments": 245, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas corticis", "strain": "strain=36D10-4-7", "accession": "GCA_012035195.1", "taxid": 2722791, "species_taxid": 2722791, "relation_to_type": "type", "validated": true, "ani": 76.8427, "matched_fragments": 249, "total_fragments": 1081, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_004681125.1", "gtdb_species": "s__Polymorphobacter_A arshaanensis", "ani": 100.0, "matched_fragments": 1080, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter_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": "conclusive" }, { "accession": "GCA_003241875.1", "gtdb_species": "s__Polymorphobacter sp003241875", "ani": 79.0563, "matched_fragments": 462, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter", "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_001295935.1", "gtdb_species": "s__Polymorphobacter sp001295935", "ani": 78.8901, "matched_fragments": 414, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter", "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_007097155.1", "gtdb_species": "s__Glacieibacterium frigidum", "ani": 78.8515, "matched_fragments": 460, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium", "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_011927825.1", "gtdb_species": "s__Polymorphobacter fuscus", "ani": 78.8121, "matched_fragments": 415, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.98", "min_intra_species_ani": "99.98", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_018982885.1", "gtdb_species": "s__CAHJWT01 sp018982885", "ani": 78.7845, "matched_fragments": 393, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01", "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_002256005.1", "gtdb_species": "s__Polymorphobacter sp002256005", "ani": 78.7633, "matched_fragments": 433, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter", "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_018982925.1", "gtdb_species": "s__Glacieibacterium sp018982925", "ani": 78.6973, "matched_fragments": 448, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Glacieibacterium", "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_903642255.1", "gtdb_species": "s__CAHJWT01 sp903642255", "ani": 78.6483, "matched_fragments": 253, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01", "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_014643455.1", "gtdb_species": "s__Polymorphobacter glacialis", "ani": 78.5805, "matched_fragments": 366, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter", "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_903643075.1", "gtdb_species": "s__CAHJWT01 sp903643075", "ani": 78.4766, "matched_fragments": 268, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01", "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_903939555.1", "gtdb_species": "s__Polymorphobacter sp903939555", "ani": 78.4483, "matched_fragments": 290, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.54", "min_intra_species_ani": "98.06", "mean_intra_species_af": "0.84", "min_intra_species_af": "0.82", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCA_019245455.1", "gtdb_species": "s__CAHJWT01 sp019245455", "ani": 78.3745, "matched_fragments": 298, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__CAHJWT01", "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_014205635.1", "gtdb_species": "s__Polymorphobacter multimanifer", "ani": 78.0859, "matched_fragments": 315, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.78", "min_intra_species_ani": "99.78", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_013410105.1", "gtdb_species": "s__Sphingopyxis sp013410105", "ani": 77.6631, "matched_fragments": 254, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.44", "min_intra_species_ani": "99.44", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_014204695.1", "gtdb_species": "s__Sphingomonas sp001897045", "ani": 77.2353, "matched_fragments": 271, "total_fragments": 1081, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.82", "min_intra_species_ani": "96.97", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.83", "num_clustered_genomes": 6, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 25.0, "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": [ "Polymorphobacter", "arshaanensis" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }