{ "type": "genome", "identifier": "GCF_002951615.1", "organism": "Rahnella sikkimica", "title": "Rahnella sikkimica", "description": "na", "data type": "Genome sequencing and assembly", "organization": "CSIR-Institute of Himalayan Bioresource Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_002951615.1", "bioproject": "PRJNA224116", "biosample": "SAMN06209637", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "1805933", "species_taxid": "1805933", "organism_name": "Rahnella sikkimica", "infraspecific_name": "strain=ERMR1:05", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2018/02/20", "asm_name": "ASM295161v1", "asm_submitter": "CSIR-Institute of Himalayan Bioresource Technology", "gbrs_paired_asm": "GCA_002951615.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/951/615/GCF_002951615.1_ASM295161v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5530672", "genome_size_ungapped": "5530672", "gc_percent": "52.500000", "replicon_count": "4", "scaffold_count": "4", "contig_count": "4", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_002951615.1-RS_2024_08_12", "annotation_date": "2024-08-12", "total_gene_count": "5093", "protein_coding_gene_count": "4865", "non_coding_gene_count": "104", "pubmed_id": "36378360" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2018-02-20", "dateModified": "2018-02-20", "datePublished": "2018-02-20", "_annotation": { "sample_count": 1, "sample_organism": [ "Rahnella sikkimica" ], "sample_taxid": [ "1805933" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "India: West Sikkim, East Rathong Glacier" ], "sample_host_location_id": [], "data_size": "1.561 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": 10.0, "max": 10.0 }, "completeness": 98.96, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5530672", "Number of Sequences": "4", "Longest Sequences (bp)": "4643505", "N50 (bp)": "4643505", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "52.7", "Number of CDSs": "5069", "Average Protein Length": "311.7", "Coding Ratio (%)": "85.7", "Number of rRNAs": "23", "Number of tRNAs": "76", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Rahnella laticis", "strain": "strain=SAP-17", "accession": "GCA_015644585.1", "taxid": 2787622, "species_taxid": 2787622, "relation_to_type": "type", "validated": true, "ani": 93.1423, "matched_fragments": 1538, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella contaminans", "strain": "strain=Lac-M11", "accession": "GCA_011065485.1", "taxid": 2703882, "species_taxid": 2703882, "relation_to_type": "type", "validated": true, "ani": 92.0726, "matched_fragments": 1457, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella victoriana", "strain": "strain=DSM 27397", "accession": "GCA_004330295.1", "taxid": 1510570, "species_taxid": 1510570, "relation_to_type": "type", "validated": true, "ani": 86.5971, "matched_fragments": 1311, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella variigena", "strain": "strain=CIP 105588", "accession": "GCA_003610915.1", "taxid": 574964, "species_taxid": 574964, "relation_to_type": "type", 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1279, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella ecdela", "strain": "strain=FRB 231", "accession": "GCA_019049625.1", "taxid": 2816250, "species_taxid": 2816250, "relation_to_type": "type", "validated": true, "ani": 86.1341, "matched_fragments": 1304, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella woolbedingensis", "strain": "strain=DSM 27399", "accession": "GCA_003602095.1", "taxid": 1510574, "species_taxid": 1510574, "relation_to_type": "type", "validated": true, "ani": 86.1268, "matched_fragments": 1311, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella aquatilis", "strain": "strain=ATCC 33071", "accession": "GCA_000735505.1", "taxid": 34038, "species_taxid": 34038, "relation_to_type": "suspected-type", "validated": true, "ani": 86.1144, "matched_fragments": 1215, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella bruchi", "strain": "strain=DSM 27398", "accession": "GCA_003614975.1", "taxid": 1510573, "species_taxid": 1510573, "relation_to_type": "type", "validated": true, "ani": 86.114, "matched_fragments": 1308, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella rivi", "strain": "strain=FC061912-K", "accession": "GCA_019049655.1", "taxid": 2816249, "species_taxid": 2816249, "relation_to_type": "type", "validated": true, "ani": 85.7021, "matched_fragments": 1300, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella inusitata", "strain": "strain=DSM 30078", "accession": "GCA_003263515.1", "taxid": 58169, "species_taxid": 58169, "relation_to_type": "type", "validated": true, "ani": 85.5461, "matched_fragments": 1228, "total_fragments": 1841, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Rahnella 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"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_015644585.1", "gtdb_species": "s__Rahnella laticis", "ani": 93.1423, "matched_fragments": 1538, "total_fragments": 1841, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.65", "min_intra_species_ani": "95.20", "mean_intra_species_af": "0.90", "min_intra_species_af": "0.83", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_002834385.1", "gtdb_species": "s__Rahnella sp002834385", "ani": 90.1402, "matched_fragments": 1444, "total_fragments": 1841, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Rahnella", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": 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