relecov_2026_drylab_eqa/flu_sample_metadata_example.json at main · BU-ISCIII/relecov_2026_drylab_eqa · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
{
    "batch_id": "ALL_FILES",
    "bioinformatics_analysis_date": "2026-02-05",
    "bioinformatics_protocol_software_name": "IRMA",
    "bioinformatics_protocol_software_version": "v1.3.1",
    "clade_assignment": "2.3.4.4b",
    "clade_assignment_date": "2026-02-06",
    "clade_assignment_software_database_version": "2025-09-09--12-13-13Z",
    "clade_assignment_software_name": "Nextclade",
    "clade_assignment_software_version": "3.9.1",
    "collecting_lab_sample_id": "FLU1",
    "commercial_open_source_both": "Open Source [SWO:1000008]",
    "consensus_genome_length": "13136",
    "consensus_params": "MIN_AMBIG=0.75; MIN_CONS_SUPPORT=9",
    "consensus_sequence_filename": "FLU1.consensus.fa",
    "consensus_sequence_md5": "c8360565ca6b9e4e6a1077ef92bb5433",
    "consensus_sequence_name": "A/FLU1_HA,A/FLU1_MP,A/FLU1_NS,A/FLU1_NA,A/FLU1_PB2,A/FLU1_PB1,A/FLU1_PA,A/FLU1_NP",
    "consensus_sequence_software_name": "IRMA consensus",
    "consensus_sequence_software_version": "v1.3.1",
    "dehosting_method_software_name": "Kraken2",
    "dehosting_method_software_version": "2.1.3",
    "depth_of_coverage_threshold": "10x",
    "depth_of_coverage_value": 220224,
    "enrichment_panel": "CommonUni12/13 universal primers (Van den Hoecke 2015)",
    "enrichment_panel_version": "CommonUni12/13 universal primers (Van den Hoecke 2015) v1.0",
    "enrichment_protocol": "Amplicon [GENEPIO:0001974]",
    "file_format": "FASTQ [EDAM:1930]",
    "library_layout": "Paired-end [OBI:0001852]",
    "lineage_assignment_database_version": "0000",
    "number_of_Ns": 0,
    "number_of_reads_sequenced": 28411290,
    "number_of_unambiguous_bases": 13136,
    "number_of_variants_in_consensus": 1377,
    "number_of_variants_with_effect": 0,
    "organism": "Influenza virus [SNOMED:725894000]",
    "pass_reads": 28166074,
    "per_Ns": 0.0,
    "per_genome_greater_10x": 96.57,
    "per_reads_host": 17.8,
    "per_reads_virus": 74.04,
    "per_unmapped": 8.16,
    "preprocessing_params": "--cut_front --cut_tail --cut_mean_quality 15 --qualified_quality_phred 15 --trim_poly_x --length_required 50 --detect_adapter_for_pe",
    "preprocessing_software_name": "Fastp",
    "preprocessing_software_version": "v0.20.0",
    "qc_test": "Pass",
    "read_length": 151,
    "reference_genome_accession": "AF144305.1,AF144306.1,AF144307.1,AF144304.1,AF144300.1,AF144301.1,AF144302.1,AF144303.1",
    "sequence_file_R1": "FLU1_R1.fastq",
    "sequence_file_R1_md5": "85508ed5cef75d52a0461b92329fbf32",
    "sequence_file_R2": "FLU1_R2.fastq",
    "sequence_file_R2_md5": "02886ba1b30e8b021c87c707eb25f42d",
    "sequence_file_path_R1": "/data/ucct/bi/research/EQA_RELECOV_2026/RAW_READS/ALL_FILES",
    "sequence_file_path_R2": "/data/ucct/bi/research/EQA_RELECOV_2026/RAW_READS/ALL_FILES",
    "sequencing_instrument_model": "Illumina MiSeq [OBI:0002003]",
    "sequencing_instrument_platform": "Illumina [OBI:0000759]",
    "submitting_institution_id": "COD-2400",
    "subtype_assignment": "H5N1",
    "subtype_assignment_software_database_version": "0000",
    "subtype_assignment_software_name": "IRMA subtyping",
    "subtype_assignment_software_version": "v1.3.1",
    "type_assignment": "A",
    "type_assignment_software_database_version": "0000",
    "type_assignment_software_name": "IRMA typing",
    "type_assignment_software_version": "v1.3.1",
    "variant_calling_params": "-f 0.25 -d 10",
    "variant_calling_software_name": "Custom variant calling script",
    "vcf_filename": "FLU1_HA.vcf,FLU1_MP.vcf,FLU1_NA.vcf,FLU1_NP.vcf,FLU1_NS.vcf,FLU1_PA.vcf,FLU1_PB1.vcf,FLU1_PB2.vcf"
}