{ "type": "genome", "identifier": "GCF_003194385.1", "organism": "Pokkaliibacter plantistimulans", "title": "Pokkaliibacter plantistimulans", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Microbial Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_003194385.1", "bioproject": "PRJNA224116", "biosample": "SAMN03447955", "wgs_master": "LAPT00000000.1", "refseq_category": "reference genome", "taxid": "1635171", "species_taxid": "1635171", "organism_name": "Pokkaliibacter plantistimulans", "infraspecific_name": "strain=L1E11", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/06/06", "asm_name": "ASM319438v1", "asm_submitter": "CSIR-Institute of Microbial Technology", "gbrs_paired_asm": "GCA_003194385.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/194/385/GCF_003194385.1_ASM319438v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5791196", "genome_size_ungapped": "5791196", "gc_percent": "56.000000", "replicon_count": "0", "scaffold_count": "216", "contig_count": "216", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_003194385.1-RS_2024_04_15", "annotation_date": "2024-04-15", "total_gene_count": "5196", "protein_coding_gene_count": "5045", "non_coding_gene_count": "89", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-06-06", "dateModified": "2018-06-06", "datePublished": "2018-06-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Pokkaliibacter plantistimulans" ], "sample_taxid": [ "1635171" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India" ], "sample_host_location_id": [], "data_size": "1.649 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)": "5791196", "Number of Sequences": "216", "Longest Sequences (bp)": "133978", "N50 (bp)": "53297", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "55.8", "Number of CDSs": "5086", "Average Protein Length": "319.4", "Coding Ratio (%)": "84.2", "Number of rRNAs": "5", "Number of tRNAs": "77", "Number of CRISPRs": "8" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Pokkaliibacter plantistimulans", "strain": "strain=L1E11", "accession": "GCA_003194385.1", "taxid": 1635171, "species_taxid": 1635171, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1814, "total_fragments": 1826, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Marinobacterium lutimaris", "strain": "strain=DSM 22012", "accession": "GCA_900108065.1", "taxid": 568106, "species_taxid": 568106, "relation_to_type": "type", "validated": true, "ani": 76.4916, "matched_fragments": 145, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium mangrovicola", "strain": "strain=DSM 27697", "accession": "GCA_004339595.1", "taxid": 1476959, "species_taxid": 1476959, "relation_to_type": "type", "validated": true, "ani": 76.4859, "matched_fragments": 126, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrincola iocasae", "strain": "strain=KXZD1103", "accession": "GCA_008727795.1", "taxid": 2614693, "species_taxid": 2614693, "relation_to_type": "type", "validated": true, "ani": 76.4223, "matched_fragments": 51, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium arenosum", "strain": "strain=CAU 1594", "accession": "GCA_019795155.1", "taxid": 2862496, "species_taxid": 2862496, "relation_to_type": "type", "validated": true, "ani": 76.3275, "matched_fragments": 120, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium zhoushanense", "strain": "strain=CGMCC 1.15341", "accession": "GCA_014641945.1", "taxid": 1679163, "species_taxid": 1679163, "relation_to_type": "type", "validated": true, "ani": 76.3195, "matched_fragments": 119, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium aestuarii", "strain": "strain=ST58-10", "accession": "GCA_001651805.1", "taxid": 1821621, "species_taxid": 1821621, "relation_to_type": "type", "validated": true, "ani": 76.3195, "matched_fragments": 137, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Endozoicomonas montiporae", "strain": "strain=CL-33", "accession": "GCA_001583435.1", "taxid": 1027273, "species_taxid": 1027273, "relation_to_type": "type", "validated": true, "ani": 76.2542, "matched_fragments": 50, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter halophilus", "strain": "strain=JCM 30472", "accession": "GCA_003007685.1", "taxid": 1323740, "species_taxid": 1323740, "relation_to_type": "type", "validated": true, "ani": 76.2179, "matched_fragments": 55, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter halophilus", "strain": "strain=CGMCC 1.12481", "accession": "GCA_014637865.1", "taxid": 1323740, "species_taxid": 1323740, "relation_to_type": "type", "validated": true, "ani": 76.1904, "matched_fragments": 56, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphritea atlantica", "strain": "strain=DSM 18887", "accession": "GCA_900111095.1", "taxid": 355243, "species_taxid": 355243, "relation_to_type": "type", "validated": true, "ani": 76.1739, "matched_fragments": 58, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Endozoicomonas montiporae", "strain": "strain=LMG 24815", "accession": "GCA_000722565.1", "taxid": 1027273, "species_taxid": 1027273, "relation_to_type": "type", "validated": true, "ani": 76.1568, "matched_fragments": 51, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Oceanobacter mangrovi", "strain": "strain=SM2-42", "accession": "GCA_019740315.1", "taxid": 2862510, "species_taxid": 2862510, "relation_to_type": "type", "validated": true, "ani": 76.1108, "matched_fragments": 89, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas stutzeri", "strain": "strain=FDAARGOS_875", "accession": "GCA_016028655.1", "taxid": 316, "species_taxid": 316, "relation_to_type": "type", "validated": true, "ani": 76.1017, "matched_fragments": 102, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Stutzerimonas stutzeri", "strain": "strain=CGMCC 1.1803", "accession": "GCA_000219605.1", "taxid": 316, "species_taxid": 316, "relation_to_type": "type", "validated": true, "ani": 76.0847, "matched_fragments": 102, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter denitrificans", "strain": "strain=JB02H27", "accession": "GCA_008795955.1", "taxid": 2597703, "species_taxid": 2597703, "relation_to_type": "type", "validated": true, "ani": 76.0658, "matched_fragments": 51, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas capeferrum", "strain": "strain=WCS358", "accession": "GCA_022548835.1", "taxid": 1495066, "species_taxid": 1495066, "relation_to_type": "type", "validated": true, "ani": 76.0257, "matched_fragments": 111, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium rhizophilum", "strain": "strain=DSM 18822", "accession": "GCA_000378045.1", "taxid": 420402, "species_taxid": 420402, "relation_to_type": "type", "validated": true, "ani": 75.9616, "matched_fragments": 128, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacterium jannaschii", "strain": "strain=DSM 6295", "accession": "GCA_000620085.1", "taxid": 64970, "species_taxid": 64970, "relation_to_type": "type", "validated": true, "ani": 75.945, "matched_fragments": 123, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas jessenii", "strain": "strain=DSM 17150", "accession": "GCA_002236115.1", "taxid": 77298, "species_taxid": 77298, "relation_to_type": "suspected-type", "validated": true, "ani": 75.9378, "matched_fragments": 112, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Nitrincola lacisaponensis", "strain": "strain=4CA", "accession": "GCA_000691225.1", "taxid": 267850, "species_taxid": 267850, "relation_to_type": "type", "validated": true, "ani": 75.9324, "matched_fragments": 75, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Amphritea pacifica", "strain": "strain=ZJ14W", "accession": "GCA_016924145.1", "taxid": 2811233, "species_taxid": 2811233, "relation_to_type": "type", "validated": true, "ani": 75.9245, "matched_fragments": 68, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas caricapapayae", "strain": "strain=ICMP2855", "accession": "GCA_001400735.1", "taxid": 46678, "species_taxid": 46678, "relation_to_type": "type", 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"matched_fragments": 65, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Pseudomonas faucium", "strain": "strain=BML-PP048", "accession": "GCA_013373935.1", "taxid": 2740518, "species_taxid": 2740518, "relation_to_type": "type", "validated": true, "ani": 75.7575, "matched_fragments": 114, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Marinobacter subterrani", "strain": "strain=JG233", "accession": "GCA_001045555.1", "taxid": 1658765, "species_taxid": 1658765, "relation_to_type": "type", "validated": true, "ani": 75.7234, "matched_fragments": 64, "total_fragments": 1826, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_003194385.1", "gtdb_species": "s__Pokkaliibacter plantistimulans", "ani": 100.0, "matched_fragments": 1814, "total_fragments": 1826, 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