{ "type": "genome", "identifier": "GCF_000576305.1", "organism": "Paenibacillus pini JCM 16418", "title": "Paenibacillus pini JCM 16418", "description": "na", "data type": "Genome sequencing and assembly", "organization": "The University of Tokyo", "publication": [ {} ], "properties": { "assembly_accession": "GCF_000576305.1", "bioproject": "PRJNA224116", "biosample": "SAMD00000453", "wgs_master": "BAVZ00000000.1", "refseq_category": "reference genome", "taxid": "1236976", "species_taxid": "669461", "organism_name": "Paenibacillus pini JCM 16418", "infraspecific_name": "strain=JCM 16418", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2014/02/17", "asm_name": "ASM57630v1", "asm_submitter": "The University of Tokyo", "gbrs_paired_asm": "GCA_000576305.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/576/305/GCF_000576305.1_ASM57630v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4961801", "genome_size_ungapped": "4961801", "gc_percent": "42.000000", "replicon_count": "0", "scaffold_count": "68", "contig_count": "68", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_000576305.1-RS_2024_09_02", "annotation_date": "2024-09-02", "total_gene_count": "4919", "protein_coding_gene_count": "4443", "non_coding_gene_count": "87", "pubmed_id": "24652984" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2014-02-17", "dateModified": "2014-02-17", "datePublished": "2014-02-17", "_annotation": { "sample_count": 1, "sample_organism": [ "Paenibacillus pini JCM 16418" ], "sample_taxid": [ "1236976" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "NA" ], "sample_host_location_id": [], "data_size": "1.418 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)": "4961801", "Number of Sequences": "68", "Longest Sequences (bp)": "671129", "N50 (bp)": "258739", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "42.0", "Number of CDSs": "5127", "Average Protein Length": "278.6", "Coding Ratio (%)": "86.4", "Number of rRNAs": "4", "Number of tRNAs": "78", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Paenibacillus pini", "strain": "strain=JCM 16418", "accession": "GCA_001315125.1", "taxid": 669461, "species_taxid": 669461, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1619, "total_fragments": 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"strain": "strain=NBRC 15958", "accession": "GCA_004001045.1", "taxid": 59846, "species_taxid": 59846, "relation_to_type": "type", "validated": true, "ani": 78.1507, "matched_fragments": 282, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus macquariensis", "strain": "strain=ATCC 23464", "accession": "GCA_900156375.1", "taxid": 948756, "species_taxid": 948756, "relation_to_type": "type", "validated": true, "ani": 77.9418, "matched_fragments": 241, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus macquariensis subsp. macquariensis", "strain": "strain=DSM 2", "accession": "GCA_001637165.1", "taxid": 1468, "species_taxid": 948756, "relation_to_type": "type", "validated": true, "ani": 77.9317, "matched_fragments": 236, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus lautus", "strain": "strain=NBRC 15380", "accession": "GCA_004000945.1", "taxid": 1401, "species_taxid": 1401, "relation_to_type": "suspected-type", "validated": true, "ani": 77.8529, "matched_fragments": 138, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus sophorae", "strain": "strain=DSM 23020", "accession": "GCA_018966525.1", "taxid": 1333845, "species_taxid": 1333845, "relation_to_type": "type", "validated": true, "ani": 77.7679, "matched_fragments": 84, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus sophorae", "strain": "strain=CGMCC 1.10238", "accession": "GCA_900110315.1", "taxid": 1333845, "species_taxid": 1333845, "relation_to_type": "type", "validated": true, "ani": 77.6501, "matched_fragments": 82, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus albidus", "strain": "strain=CGMCC 1.16134", "accession": "GCA_014644435.1", "taxid": 2041023, "species_taxid": 2041023, "relation_to_type": "type", "validated": true, "ani": 77.5718, "matched_fragments": 117, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus pabuli", "strain": "strain=NBRC 13638", "accession": "GCA_001514495.1", "taxid": 1472, "species_taxid": 1472, "relation_to_type": "suspected-type", "validated": true, "ani": 77.5556, "matched_fragments": 152, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus gallinarum", "strain": "strain=Sa2BVA9", "accession": "GCA_014836635.1", "taxid": 2762232, "species_taxid": 2762232, "relation_to_type": "type", "validated": true, "ani": 77.4664, "matched_fragments": 138, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus dakarensis", "strain": "strain=FF9", "accession": "GCA_001373415.1", "taxid": 1527293, "species_taxid": 1527293, "relation_to_type": "type", "validated": true, "ani": 77.4609, "matched_fragments": 138, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus macerans", "strain": "strain=ATCC 8244", "accession": "GCA_000746875.1", "taxid": 44252, "species_taxid": 44252, "relation_to_type": "type", "validated": true, "ani": 77.3344, "matched_fragments": 74, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Paenibacillus farraposensis", "strain": "strain=UY79", "accession": "GCA_020736845.1", "taxid": 2807095, "species_taxid": 2807095, "relation_to_type": "type", "validated": true, "ani": 77.2616, "matched_fragments": 112, "total_fragments": 1623, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_000576305.1", "gtdb_species": "s__Paenibacillus pini", "ani": 100.0, 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