turns-00031.parquet:17860
2b303e899252f2b8894553badegenerate_repetitionAbsentFinal dense release
USER
the following content is metadata for a bacteria genome sequencing data in json format, you need to extract information below from it and output in 2 rows tab-delimited format:
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accession number species name strain name isolate or collection date in yyyy-mm-dd format geographic information of islateion host name mlsty type serotype
xxxx xxxx xxxx xxxx xxxx xxxx xxxx xxxx
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1st row is column name, and xxxx is corresponding information in 2nd row.
Don't add any comments or explaining to output. If the appropriate information is not available, use "N/A" substitution; if the date has month or day, just print available information; if the host name is not available but this bacteria is a vaccine, then use "vaccine" as the host name'
#'if geographic information of islateion not avaiable, you can try to guess from submitter
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{'accession': 'GCA_029074405.1', 'annotation_info': {'method': 'Best-placed reference protein set; GeneMarkS-2+', 'name': 'NCBI Prokaryotic Genome Annotation Pipeline (PGAP)', 'pipeline': 'NCBI Prokaryotic Genome Annotation Pipeline (PGAP)', 'provider': 'NCBI', 'release_date': '2023-02-10', 'software_version': '6.4', 'stats': {'gene_counts': {'non_coding': 64, 'protein_coding': 1680, 'pseudogene': 12, 'total': 1756}}}, 'assembly_info': {'assembly_level': 'Scaffold', 'assembly_method': 'SPAdes v. 3.11.1', 'assembly_name': 'ASM2907440v1', 'assembly_status': 'current', 'assembly_type': 'haploid', 'bioproject_accession': 'PRJNA909344', 'bioproject_lineage': [{'bioprojects': [{'accession': 'PRJNA909344', 'title': 'Population Structure and Genomic Characteristics of Australian Erysipelothrix rhusiopathiae'}]}], 'biosample': {'accession': 'SAMN32081866', 'attributes': [{'name': 'strain', 'value': 'EMAI_53'}, {'name': 'host', 'value': 'fish'}, {'name': 'collection_date', 'value': '1988-03-02'}, {'name': 'geo_loc_name', 'value': 'Germany'}, {'name': 'sample_type', 'value': 'Cell Culture'}, {'name': 'genotype', 'value': 'MLST:9'}], 'bioprojects': [{'accession': 'PRJNA909344'}], 'description': {'organism': {'organism_name': 'Erysipelothrix rhusiopathiae', 'tax_id': 1648}, 'title': 'Microbe sample from Erysipelothrix rhusiopathiae'}, 'last_updated': '2023-03-20T23:01:09.503', 'models': ['Microbe, viral or environmental'], 'owner': {'contacts': [{}], 'name': 'Deparment of Primary Industries NSW'}, 'package': 'Microbe.1.0', 'publication_date': '2023-03-10T12:41:20.960', 'sample_ids': [{'label': 'Sample name', 'value': 'erysip_53'}, {'db': 'SRA', 'value': 'SRS17098938'}], 'status': {'status': 'live', 'when': '2023-03-10T12:41:20.960'}, 'submission_date': '2022-12-06T20:42:04.570'}, 'comments': 'The annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Information about PGAP can be found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/', 'genome_notes': ['from large multi-isolate project'], 'paired_assembly': {'accession': 'GCF_029074405.1', 'annotation_name': 'NCBI Prokaryotic Genome Annotation Pipeline (PGAP)', 'status': 'suppressed'}, 'release_date': '2023-03-09', 'sequencing_tech': 'Illumina MiSeq', 'submitter': 'Deparment of Primary Industries NSW'}, 'assembly_stats': {'contig_l50': 4, 'contig_n50': 159655, 'gc_count': '644628', 'gc_percent': 36.5, 'genome_coverage': '31.8x', 'number_of_component_sequences': 35, 'number_of_contigs': 36, 'number_of_scaffolds': 35, 'scaffold_l50': 4, 'scaffold_n50': 159655, 'total_sequence_length': '1772039', 'total_ungapped_length': '1771944'}, 'average_nucleotide_identity': {'best_ani_match': {'ani': 99.57, 'assembly': 'GCA_000160815.2', 'assembly_coverage': 95.48, 'category': 'type', 'organism_name': 'Erysipelothrix rhusiopathiae', 'type_assembly_coverage': 96.88}, 'category': 'category_na', 'comment': 'na', 'match_status': 'species_match', 'submitted_ani_match': {'ani': 99.57, 'assembly': 'GCA_000160815.2', 'assembly_coverage': 95.48, 'category': 'type', 'organism_name': 'Erysipelothrix rhusiopathiae ATCC 19414', 'type_assembly_coverage': 96.88}, 'submitted_organism': 'Erysipelothrix rhusiopathiae', 'submitted_species': 'Erysipelothrix rhusiopathiae', 'taxonomy_check_status': 'OK'}, 'checkm_info': {'checkm_marker_set': 'Erysipelothrix', 'checkm_marker_set_rank': 'genus', 'checkm_species_tax_id': 1648, 'checkm_version': 'v1.2.2', 'completeness': 93.71, 'completeness_percentile': 66.96832, 'contamination': 1.44}, 'current_accession': 'GCA_029074405.1', 'organism': {'infraspecific_names': {'strain': 'EMAI_53'}, 'organism_name': 'Erysipelothrix rhusiopathiae', 'tax_id': 1648}, 'paired_accession': 'GCF_029074405.1', 'source_database': 'SOURCE_DATABASE_GENBANK', 'wgs_info': {'master_wgs_url': 'https://www.ncbi.nlm.nih.gov/nuccore/JAQTDS000000000.1', 'wgs_contigs_url': 'https://www.ncbi.nlm.nih.gov/Traces/wgs/JAQTDS01', 'wgs_project_accession': 'JAQTDS01'}}ASSISTANT
``` accession number species name strain name isolate or collection date in yyyy-mm-dd format geographic information of islateion host name mlsty type serotype GCA_029074405.1 Erysipelothrix rhusiopathiae EMAI_53 1988-03-02 Germany fish MLST:9 N/A ```