{ "type": "genome", "identifier": "GCF_019880585.1", "organism": "Sphingomonas colocasiae", "title": "Sphingomonas colocasiae", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Life sciences Institute", "publication": [ {} ], "properties": { "assembly_accession": "GCF_019880585.1", "bioproject": "PRJNA224116", "biosample": "SAMN21032053", "wgs_master": "JAINVV000000000.1", "refseq_category": "reference genome", "taxid": "1848973", "species_taxid": "1848973", "organism_name": "Sphingomonas colocasiae", "infraspecific_name": "strain=JCM 31229", "isolate": "na", "version_status": "latest", "assembly_level": "Contig", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2021/09/05", "asm_name": "ASM1988058v1", "asm_submitter": "Life sciences Institute", "gbrs_paired_asm": "GCA_019880585.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/019/880/585/GCF_019880585.1_ASM1988058v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "6569909", "genome_size_ungapped": "6569909", "gc_percent": "65.500000", "replicon_count": "0", "scaffold_count": "23", "contig_count": "23", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_019880585.1-RS_2024_05_06", "annotation_date": "2024-05-06", "total_gene_count": "5941", "protein_coding_gene_count": "5854", "non_coding_gene_count": "57", "pubmed_id": "na" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2021-09-05", "dateModified": "2021-09-05", "datePublished": "2021-09-05", "_annotation": { "sample_count": 1, "sample_organism": [ "Sphingomonas colocasiae" ], "sample_taxid": [ "1848973" ], "sample_host_organism": [ "Colocasia esculenta (taro)" ], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "China: Taiwan" ], "sample_host_location_id": [], "data_size": "1.788 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)": "6569909", "Number of Sequences": "23", "Longest Sequences (bp)": "1376521", "N50 (bp)": "622686", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "65.6", "Number of CDSs": "5906", "Average Protein Length": "336.5", "Coding Ratio (%)": "90.8", "Number of rRNAs": "3", "Number of tRNAs": "56", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Sphingomonas colocasiae", "strain": "strain=JCM 31229", "accession": "GCA_019880585.1", "taxid": 1848973, "species_taxid": 1848973, "relation_to_type": "type", "validated": true, "ani": 100.0, 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"ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas leidyi", "strain": "strain=DSM 4733", "accession": "GCA_011761945.1", "taxid": 68569, "species_taxid": 68569, "relation_to_type": "type", "validated": true, "ani": 79.2066, "matched_fragments": 599, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas changnyeongensis", "strain": "strain=C33", "accession": "GCA_009913435.1", "taxid": 2698679, "species_taxid": 2698679, "relation_to_type": "type", "validated": true, "ani": 79.076, "matched_fragments": 507, "total_fragments": 2178, "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": 79.0334, "matched_fragments": 493, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas horti", "strain": "strain=MAH-20", "accession": "GCA_009753715.1", "taxid": 2682842, "species_taxid": 2682842, "relation_to_type": "type", "validated": true, "ani": 78.9479, "matched_fragments": 510, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas trueperi", "strain": "strain=DSM 7225", "accession": "GCA_011927635.1", "taxid": 53317, "species_taxid": 53317, "relation_to_type": "type", "validated": true, "ani": 78.9376, "matched_fragments": 543, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas koreensis", "strain": "strain=NBRC 16723", "accession": "GCA_001598395.1", "taxid": 93064, "species_taxid": 93064, "relation_to_type": "type", "validated": true, "ani": 78.9075, "matched_fragments": 566, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas changbaiensis", "strain": "strain=NBRC 104936", "accession": "GCA_000974765.1", "taxid": 529705, "species_taxid": 529705, "relation_to_type": "type", "validated": true, "ani": 78.8097, "matched_fragments": 463, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas desiccabilis", "strain": "strain=CP1D", "accession": "GCA_004135605.1", "taxid": 429134, "species_taxid": 429134, "relation_to_type": "type", "validated": true, "ani": 78.7587, "matched_fragments": 443, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas hylomeconis", "strain": "strain=CCTCC AB 2013304", "accession": "GCA_025370105.1", "taxid": 1395958, "species_taxid": 1395958, "relation_to_type": "type", "validated": true, "ani": 78.7352, "matched_fragments": 556, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas pituitosa", "strain": "strain=NBRC 102491", "accession": "GCA_001598435.1", "taxid": 99597, "species_taxid": 99597, "relation_to_type": "type", "validated": true, "ani": 78.7269, "matched_fragments": 537, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas soli", "strain": "strain=NBRC 100801", "accession": "GCA_001591025.1", "taxid": 266127, "species_taxid": 266127, "relation_to_type": "type", "validated": true, "ani": 78.675, "matched_fragments": 496, "total_fragments": 2178, "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": 78.6564, "matched_fragments": 520, "total_fragments": 2178, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Sphingomonas alpina", "strain": "strain=DSM 22537", "accession": "GCA_025370095.1", "taxid": 653931, "species_taxid": 653931, 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